Pure & Appi. Chem., Vol. 56, No. 5, pp. 595624, 1984.

Printed in Great Britain.

00334545/84 $3.00+0.00
Pergamon Press Ltd.

INTERNATIONAL UNION OF PURE

AND APPLIED CHEMISTRY
and

INTERNATIONAL UNION OF BIOCHEMISTRY

JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE*

NOMENCLATURE AND SYMBOLISM FOR

AMINO ACIDS AND PEPTIDES
(Recommendations 1983)

*Membershjp of the Commission (JCBN) is as follows:

Chairman: H. B. F. DIXON (UK); Secretary: A. CORNISH-BOWDEN (UK);

Members: C. LIEBECQ (Belgium as Chairman of TUB Committee of Editors of
Biochemical Journals); K. L. LOENING (USA); G. P. MOSS (UK); J. REEDIJK
(Netherlands); S. F. VELICK (USA); J. F. G. VLIEGENTHART (Netherlands).
Additional contributors to the formulation of these recommendations:

Nomenclature Committee of IUB (NCIUB) (those additional to JCBN):

H. BIELKA (GDR); N. SHARON (Israel); E. C. WEBB (Australia).
P. KARLSON (FRG, Past Chairman of JCBN); B. KEIL (France, a former Member of

NC-TUB); W. E. COHN (USA); J. T. EDSALL (USA); J. S. MORLEY (UK);

G. T. YOUNG (UK); and Members of IUPAC Commission on Nomenclature of
Organic Chemistry.

IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)

Nomenclature and Symbolism for Amino. Acids and Peptides

Recommendations 1983

CONTENTS
Introduction
NOMENCLATURE
Part 1
Part 1, Section A: Amino-Acid Nomenclature
3AA-1 Names of Common s-Amino Acids

3AA-2

3AA-3

Formation of Semisystematic Names for Amino Acids and Derivatives

2.1 Principles of forming names
2.2 Designation of locants
2.2.1 Acyclic amino acids
2.2.2 Proline
2.2.3 Aromatic rings
2.2.4 Histidine
2.2.5 Definition of side chain
2.3 Use of the prefix 'homo'
2.4 Use of the prefix 'nor'
Configuration at the s-Carbon Atom

3.1 UseofDandL
3.2 Position of prefix
3.3 Omission of prefix
3.4 Subscripts to D and L
3.5 The RS system
3.6 Amino acids derived from amino sugars
3.7 Use of meso
3.8 Use of DL

3AA-4

Configuration at Centres other than the cs-Carbon Atom

4.1 The sequence rule
4.2 Carbohydrate prefixes
4.3 Use of cis and trans

4.4 Use of 'allo'

3AA-5

4.5 Designation of centres with unknown configurations

4.6 Other stereochemical features
Optical Rotation

Part 1, Section B: Nomenclature of Non-Peptide Derivatives of Amino Acids

3AA-6

Ionization of Functional Groups and Naming of Salts

3AA-7 Amino Acids Substituted on Nitrogen

3AA-8
3AA-9

Side Chain Modifications (excluding modifications of carboxyl or nitrogen)

Esters and Amides of the Carboxyl Group

9.1 Esters
9.2 Amides, anilides and analogous derivatives
9.3 Acyl groups

3AA-10 Carboxyl Group Modifications other than Ester and Amide Formation
10.1 Removal of the carboxyl group
10.2 Ketones
10.3 Aldehydes and alcohols

These are recommendations of the IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN), whose members are
H.B.F.Dixon (chairman), A. Cornish-Bowden (secretary), C. Libecq (as chairman of the IUB Committee of Editors of Biochemical Journals),
K. L. Loening, G. P. Moss, J. Reedijk, S.F. Velick, and J. F. G. Vliegenthart. Comments may be sent to any member of the commission, or to its
secretary: A. Cornish-Bowden, Department of Biochemistry, University of Birmingham, P.O. Box 363, Birmingham, England, B15 2TT. JCBN
thanks many who helped with drawing up the recommendations, especially P. Karlson, its former chairman, B. Keil, a former member of the
Nomenclature Committee of IUB (NCIUB), other members and former members of NCIUB, namely H. Bielka, N. Sharon and E. C. Webb,
and also W. E. Cohn, J. T. Edsall, J. S. Morley, G. T. Young, and members of the IUPAC Commission on Nomenclature of Organic Chemistry
(CNOC).

Reproduced

from Eur.J.Biochem., Vol. 138, pp.937 (1984)

by courtesy of SpringerVerlag, Heidelberg, FRG.
596

Nomenclature and symbolism for amino acids and peptides

Part 1,

Section C: Peptide Nomenclature

3AA-11 Definitions of Peptides

3AA-12 Amino-Acid Residues
12.1 Definitions of residues
12.2 Ionized forms of residues

3AA-1 3 The Naming of Peptides

13.1 Construction of names
13.2 Use of prefixes in peptide names
13.3 Names of simple polymers of amino acids
13.4 Numbering of peptide atoms
13.5 Prefixes formed from peptide names
13.6 Conformations of polypeptide chains

SYMBOLISM

Part 2,

Part 2, Section A: The Three-Letter System

3AA-14 General Considerations on Three-Letter Symbols

3AA-15 Symbols for Amino Acids

15.1 Symbols for common amino acids
15.2 Symbols for less common peptide constituents
15.2.1 Hydroxyamino acids
15.2.2 Alloisoleucine and allothreonine
15.2.3 'Nor' amino acids
15.2.4 'Homo' amino acids
15.2.5 Higher unbranched amino acids
15.2.6 Carboxylated and oxidized amino acids
15.2.7 Non-amino-acid residues in peptides
3AA-16 Symbolism of Amino-Acid Residues
16.1 General principles for symbolizing residues
16.2 Lack of hydrogen on the 2-amino group
16.3 Lack of hydroxyl on the 1-carboxyl group
16.4 Removal of groups from side chains
16.4.1 Monocarboxylic acids
16.4.2 Dicarboxylic acids
16.5 Cyclic derivatives of amino acids

3AA-17 Substituted Amino Acids

17.1 Substitution in the 2-amino and 1-carboxyl groups
17.2 Substitution on side-chain functional groups
17.3 Substitution on side-chain skeletion
17.4 The use of symbols in representing reactions of side chains
17.5 Modified residues in natural peptides
17.6 Lack of substitution

3AA-18 Symbols for Substituents

18.1 Use of symbols
18.2 Principles of symbolizing substituent groups and reagents

3AA-19 Peptide Symbolism

19.1 Peptide chains

19.2 Use of configurational prefixes
19.3 Representation of charges on peptides
19.4 Peptides substituted at N-2
19.5 Cyclic peptides
19.5.1 Homodetic cyclic peptides
19.5.2 Heterodetic cyclic peptides
19.6 Depsipeptides
19.7 Peptide analogues
19.8 Alignment of peptide and nucleic-acid sequences
Part 2, Section B: The One-Letter System
3AA-20 The Need for a Concise Representation of Sequence
20.1 General considerations on the one-letter system
20.2 Limits of application of the one-letter system

3AA-21 Description of the One-Letter System

21.1 Use of the code

21.2 The code symbols

21.3 Spacing
21.4 Known sequences
21.5 Punctuation in partly known sequences

Part 3,

MODIFICATION OF NAMED PEPTIDES

3AA-22 Names and Symbols for Derivatives of Named Peptides
22.1 Replacement of residues
22.2 Extension of the peptide chain
22.3 Insertion of residues

597

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IUPACIUB JOINT CONNISSION ON BIOCHEMICAL NOMENCLATURE

22.4 Removal of residues
22.5 Substitution of side chains of residues
22.5.1 Acylation of a side-chain amino group
22.5.2 Other substituents named as prefixes

22.5.3 Acylation by a side-chain carboxyl group

22.6 Partial sequences (fragments)
22.7 Peptides with reversed sequence and enantiomers
22.8 Peptide analogues
22.9 Summary of modification nomenclature
References
Appendix

Amino Acids with Trivial Names

INTRODUCTION
The traditional and well-known names of the common a-amino acids were, in general, given to them by their discoverers and
bear no relationship to their chemical structures [1, 2]. The modification of these names to accommodate derivatives and to
designate configuration was codified in 1947 [3] and revised in 1960 [4]. After proposals for the revision of the rules for naming
a-amino acids with two centres of chirality had appeared in 1963 [5], a complete revision of the rules was made in 1974 [6} on the
basis of a report by a committee convened by H. B. Vickery. Recommendations for symbols for amino-acid residues in peptide
sequences made by Brand & Edsall(p. 224 in [8]) were revised in 1966 [9] and 1971 [10], and recommendations for a one-letter
notation were approved in 1968 [1 1 ]. Recommendations for naming and symbolizing sequences derived from those of named
peptides were made in 1966 [12].
The present revision combines all these documents. In Part I on nomenclature, the main changes are to propose names for
particular ionic forms ofresidues(3AA-12.2) and to apply the stereochemicairules [13]more fully(3AA-3). Part 2 on symbolism
introduces a few new symbols (3AA-15.2.7), simplifies the designation of ionized forms of peptides (3AA-19.3), explains the
principles for giving symbols to reagents (3AA-1 8.2), presents a method for showing how parts ofresidues react (3AA-17.4), and
describes the one-letter system for representing long sequences (3AA-2O and -21). Part 3, on the modflcation of named peptides, is
extended to cover enantiomers and reversed sequences (3AA-22.7) and peptide analogues (3AA-22.8). Symbols for the twenty
ribosomally incorporated (coded) amino acids are given in Table 1, and symbols used in these recommendations for other amino
acids are mostly listed in the Appendix, although a few others are given in 3AA-1 5.2. Substantially new recommendations are
marked by triangles in the margins.

Part 1. Nomenclature

Part 1, Section A: AMINO-ACID NOMENCLATURE

3AA-1. NAMES OF COMMON a-AMINO ACIDS

The trivial names of the a-amino acids that are commonly found in proteins and are represented in the genetic code, together
with their symbols, systematic names [14] and formulas, are given in Table 1. Some other common amino acids are listed in the
Appendix.
When the phrase 'amino acid' is a qualified noun it contains no hyphen; a hyphen is inserted when it becomes an adjective so
as to join its components in qualifying another noun, e.g. amino-acid sequence.
3AA-2. FORMATION OF SEMISYSTEMATIC NAMES FOR AMINO ACIDS AND DERIVATIVES

3AA-2.1. Principles of Forming Names

Semisystematic names of substituted a-amino acids are formed according to the general principles of organic nomenclature
[14], by attaching the name of the substituent group to the trivial name of the amino acid. The position of the substitution is
indicated by locants (see 3AA-2.2). The configuration, if known, should be indicated (see 3AA-3, 3AA-4).
New trivial names should not be coined for newly discovered a-amino acids unless there are compelling reasons. When they
are needed (e.g. because the substance is important and its semisystematic name is cumbersome), the name should be constructed
according to the general principles for naming natural products [15], including either some element of its chemical structure or
reference to its biological origin. It is important to use no elements in the trivial name that imply an incorrect structure; when a
new trivial name is used, it is essential that it be defined by a correctly constructed systematic or semisystematic name.
A number of existing trivial names are given in the Appendix, and an extensive list has been published previously [6].
3AA-2.2 Designation of Locants
Note. The atom numbering given below is the normal chemical system for designating locants. A somewhat different system
has been recommended for describing polypeptide conformations [16], in which Greek letters are used irrespective of the nature
of the atom (unless it is hydrogen), so that in lysine N-6 becomes NC, and in phenylalanine C-I, C-2 and C-6 become C, Co! and
Co2 respectively.

Nomenclature and symbolism for amino acids and peptides

599

Table 1. a-Amino acids incorporated into protein under mRNA direction

The systematic names and formulas given refer to hypothetical forms in which amino groups are unprotonated and carboxyl groups are
undissociated. This convention is useful to avoid various nomenclatural problems but should not be taken to imply that these structures represent
an appreciable fraction of the amino-acid molecules.

Trivial nam#

Symbol

One-letter
symbolb

Systematic namea

Formula

Alanine

Ala
Arg

CH3CH(NH2)COOH

ASfld

A5pd

Nd
Dd

Cys

Glnd

Qd

Glud

Ed

Gly
His

G
H

2-Aminopropanoic acid
2-Amino-5-guanidinopentanoic acid
2-Amino-3-carbamoylpropanoic acid
2-Aminobutanedioic acid
2-Amino-3-mercaptopropanoic acid
2-Amino-4-carbamoylbutanoic acid
2-Aminopentanedioic acid
Aminoethanoic acid
2-Amino-3-(1H-imidazol-4-yl)propanoic acid

Arginine
Asparagine
Aspartic acid
Cysteine
Glutamine
Glutamic acid
Glycine
Histidine

H2N-C(= NH)NH[CH2]3-CH(NH2)--COOH
H2NCOCH2CH(NH2)COOH

HOOCCH2---CH(NH2)COOH
HSCH2CH(NH2)COOH
H2NCO[CH2]2-CH(NH2)--COOH
HOOC[CH2kCH(NH2)--COOH
CH2(NH2)COOH

/CH =CCH2CH(NH2)COOH
HN

CH
Isoleucine
Leucine

Ile

Leu

Lysine

Lys

Methionine
Phenylalanine
Proline

Met
Phe
Pro

L
K
M

Serine
Threonine

Ser

Thr
Trp

F
P

2-Amino-3-methylpentanoic acida
2-Amino-4-methylpentanoic acid
2,6-Diaminohexanoic acid
2-Amino-4-(methylthio)butanoic acid
2-Amino-3-phenylpropanoic acid
Pyrrolidine-2-carboxylic acid

C2H5CH(CH3)CH(NH2}-COOH
(CH3)2CHCH2--CH(NH2)COOH
H2N[CH2].CH(NH2)COOH

2-Amino-3-hydroxypropanoic acid
2-Amino-3-hydroxybutanoic acida
2-Amino-3-(1H-indol-3-yl)propanoic acid

HOCH2CH(NH2)COOH

CH3S--[CH212CH(NH2)COOH
C6H5 CH2CH(NH2)COOH

1CH2CH2
CH-COOH
CH2

NH"

Tryptophan

CH3CH(OH)CH(NH2)COOH

EJIl.CH2CH(NH2)COOH

Tyrosine

Tyr

2-Amino-3-(4-hydroxyphenyl)propanoic acid

Valine

Val

2-Amino-3-methylbutanoic acid

Unspecified
amino acid

Xaa

Ho__/I_. cH2dH(NH2)COOH
(CH3)2CHCH(NH2)COOH

a The trivial name refers to the L or D or Dr-amino acid; for those that are chiral only the i-amino acid is used for protein biosynthesis.
Use of the one-letter symbols should be restricted to the comparison of long sequences (3AA-20).
The fully systematic forms ethanoic, propanoic, butanoic and pentanoic may alternatively be called acetic, propionic, butyric and valeric,
respectively. Similarly, butanedioic succinic, 3-carbamoylpropanoic succinamic, pentanedioic glutaric, and 4-carbamoylbutanoic glutaramic.
d The symbol Asx denotes Asp or Asn; likewise B denotes N or D. Glx and Z likewise represent glutamic acid or glutamine or a substance,
such as 4-carboxyglutamic acid, Gla (3AA-15.2.6), or 5-oxoproline, Glp (3AA-16.5), that yields glutamic acid on acid hydrolysis of peptides.
See 3AA-3 and -4 for stereochemical designation.

2.2.1. Acyclic Amino Acids

In acyclic amino acids, the carbon atom of the carboxyl group next to the carbon atom carrying the amino group is numbered
1. Alternatively, Greek letters may be used, with C-2 being designated a. This practice is not encouraged for locants, although

terms like 'a-amino acids' and 'a-carbon atom' are retained. Example:
4
3
2
1
5
6
lysine H3W-CH2-CH2--CH2-CH2-CH(NH2)--COO
a
5
y

A heteroatom has the same number as the carbon atom to which it is attached, e.g. N-2 is on C-2. When such numerals are used as
A

locants they may be written as N6- or as 6-N, e.g. N6-acetyllysine.

The carbon atoms of the methyl groups of valine are numbered 4 and 4'; likewise those of leucine are 5 and 5'. Isoleucine is
numbered as follows:
1

H3
CH3-CH2-CH--CH(NHfl-COO
4
2
1
3
5

IUPACIUB JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE

600

The word 'methyl' can be italicized for use as a locant for substitution on (or isotopic modification {Section H in [14]} of) the
A methyl group of methionine, e.g. [methyl-14C]methionine. The nitrogen atoms of arginine are designated as shown for the
arginine (1 +)cation:
a
coH2N

C-NH-[CH2]3-CH(NH3 )COO

w'H2N

It should be noted that the w and w' atoms ofthis cation are equivalent because ofresonance. The carbon atom in the guanidino
group may be called guanidinoC (it may be needed as a locant for isotopic replacement although it cannot carry a substituent).

2.2.2. Proline
The carbon atoms in proline are numbered as in pyrrolidine, the nitrogen atom being numbered 1, and proceeding towards
the carboxyl group.

NH2

Aromatic Rings

2.2.3.

The carbon atoms in the aromatic rings of phenylalanine, tyrosine and tryptophan are numbered as in systematic
nomenclature, with 1 (or 3 for tryptophan) designating the carbon atom bearing the aliphatic chain. The carbon atoms of this
chain are designated a (for the carbon atom attached to the amino and carboxyl groups) and fJ (for the atom attached to the ring
system).
Note. This numbering should also be used for decarboxylated products (e.g. tryptamine).
4

-CH(NH3)COO

HO_fILCH2 CH(NH3)COO
tyrosine

phenylalanine

a
CH2CH(NH3)COO13

fl1\2
6L9NI
H
tryptophan
2.2.4

Histidine

The nitrogen atoms of the imidazole ring of histidine are denoted by pros ('near', abbreviated it) and tele ('far', abbreviated x)
to show their position relative to the side chain. This recommendation [6, 10] arose from the fact that two different systems of
numbering the atoms in the imidazole ring of histidine had both been used for a considerable time (biochemists generally
numbering as 1 the nitrogen atom adjacent to the side chain, and organic chemists designating it as 3). The carbon atom between
the two ring nitrogen atoms is numbered 2 (as in imidazole), and the carbon atom next to the t nitrogen is numbered 5. The carbon
atoms of the aliphatic chain are designated a and /3 as in 2.2.1 and 2.2.3 above. This numbering should also be used for the
decarboxylation product histamine and for substituted histidine.
a
13
CH2CH(NH3ICOO

HNN
histidine

2.2.5.

Definition of Side Chain

A When amino acids are combined in proteins and peptides, C-i, C-2 and N-2 of each residue (the numbering being that of
aliphatic amino acids) form the repeating unit of the main chain ('backbone') and the remainder forms a 'side chain'. Hence the
words 'side chain' refer to C-3 and higher numbered carbon atoms and their substituents.

3AA-2.3. Use of the Prefix 'homo'

An a-amino acid that is otherwise similar to one of the common ones (Table 1), but that contains one more methylene group
in the carbon chain, may be named by prefixing 'homo' to the name of that common amino acid. 'Homo' in the sense of a higher
homologue (F-4.5 of [15]) is commonly used for homoserine (2-amino-4-hydroxybutanoic acid) and homocysteine (2-amino-4mercaptobutanoic acid).

3AA-2.4. Use of the Prefix 'nor'

The prefix 'nor' denotes removal of a methylene group (Sections F-4.2 and F-4.4 of [15]), but this is not the sense in which it
has been used in the names 'norvaline' and 'norleucine'. Such names, although widely used, may therefore be misinterpreted, so

Nomenclature and symbolism for amino acids and peptides

we cannot recommend them, especially since the systematic names for the compounds intended, 2-aminopentanoic acid and 2-

aminohexanoic acid, are short.

3AA-3. CONFIGURATION AT THE a-CARBON ATOM

3AA-3.1. Use OfD and L

The absolute configuration at the a-carbon atom ofthe a-amino acids is designated by the prefixed small capitalletter D or L to
indicate a formal relationship to n or L-serine and thus to i- or L-glyceraldehyde. The prefix (Greek xi) indicates unknown
configuration.
The structures ofamino acids may be drawn to show configuration in several ways [13]. In the Fischer-Rosanoff convention
each chiral centre is projected onto the plane of the paper in the orientation such that the central atom appears as the point of
intersection oftwo straightlinesjoining the attached groups in pairs, so that one straight line (which should be vertical)joins three
atoms ofthe principal chain. The central atom is then considered to lie in the plane ofthe paper, the other atoms ofthe principal
chain behind the plane from the viewer, and the remaining two groups in front of this plane. Thus an L-a-amino acid may be
represented as

cooCOOCOO
H3N_f__H or H3N.H or RLNH3+

The relationship between serine and glyceraldehyde may therefore be represented as:
CO2

CHO

HNH3 HsOH
H2OH
D-serine

CH2OH

D-glyceraldehyde

3AA-3.2. Position of Prefix

In naming a-amino acids as derivatives of substances that have well-known trivial names, the prefix L or 1) is placed
immediately before the trivial name of the parent amino acid and set off by a hyphen. Examples: trans-4-hydroxy-L-proline; 3,5diiodo-L-tyrosine.
Note. Admissible exceptions to this rule are L-hydroxyprohne and L-hydroxylysine, but only in general biochemical writing in
a context such that the position of substitution is well understood. Note further that in the names of optically active derivatives of
glycine, such as L-2-phenylglycine, the prefix must be placed before the name of the substituent as glycine itself is achiral. In the
names of salts, esters and other derivatives, including peptides, the prefix is placed immediately before the trivial name of the
parent acid or its radical. Examples: L-histidine monohydrochloride monohydrate; copper(II) L-aspartate; o-lysine dihydrochloride; N-acetyl-L-tryptophn; diethyl 1)-glutamate; N6-methyl-L-lysine.
Other semisystematic names involving a-amino-acid configurations are treated similarly. Example: S-(n-2-amino-2carboxyethyl)-o-homocysteine, or S-(t-alanin-3-yl)-r-homocysteine (3AA-8), i.e. n-cystathionine.
3AA-3.3. Omission of Prefix
The prefix may be omitted where the amino, acid is stated to be or is obviously derived from a protein source and is therefore
assumed to be L. It may also be omitted where the amino acid is synthetic and not resolved and is therefore, save in exceptional
cases, an equimolecular mixture of the enantiomers. Likewise it may be omitted in a general statement that is true for either

enantiomer or for any mixture of these.

3AA-3.4. Subscripts to D and L

Where confusion is possible between the use of the small capital letter prefix for the configuration of the a-carbon atom in
amino-acid nomenclature and for that of the highest numbered chiral carbon atom in carbohydrate nomenclature [17], a
subscript (lower case Roman letter) is added to the small capital letter prefix. If the prefix is used in the amino-acid sense, the
subscript is s (for serine); if the prefix is used in the carbohydrate sense, the subscript is g (for glyceraldehyde).
Examples: i.,-threonine, for which the synonym in carbohydrate nomenclature is 2-amino-2,4-dideoxy-Dg-threonic acid;
threonine, for which the synonym is 2-amino-2,4-dideoxy-Lg-threonic acid; i.-allothreonine, for which the synonym is 2-amino2,4-dideoxy-Lg-erythronic acid; D-allothreOnine, for which the synonym is 2-amino-2,4- dideoxy-Dg-erythronic acid.
Note that the subscripts are essential only in discussions where both amino-acid names and those of carbohydrate derivatives
occur. Nevertheless, these subscripts are highly desirable if D or L is used in naming a-amino acids that possess more than one
centre of chirality (see 3AA-4).

601

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602

3AA-3.5.

The RS System

A more general system ofstereochemical designation, which is especially convenient when there is no simple way ofrelating a
compound to a defined standard, is the RS system of Cahn, Ingold & Prelog [1 3, 1 8]. In this system the ligands of a chiral atom
are placed in an order ofpreference, based largely on atomic number. Ifthe first three ligands appear clockwise in this order when

viewed from the side remote from the least-preferred (fourth) ligand, the chiral centre is R; if anticlockwise, it is S.
The L-configuration, possessed by the chiral a-amino acids found in proteins, nearly always corresponds to Sin the RS system.

The most important exceptions are L-cysteine and L-cystine (see Appendix), which are R (in most amino acids the order of
preference of the groups around C-2 is NH, C00, R, H, but in cysteine and cystine the group R takes precedence over
carboxylate because the atomic number of sulfur attached to C-3 is higher than that of oxygen attached to C-I).
3AA-3.6. Amino Acids Derived from Amino Sugars

Amino acids that are derived from amino sugars and contain five or more carbon atoms are named in conformity with the
system of carbohydrate nomenclature [17] or with a recommended trivial name.
Examples: (1) Dg-glucOsaminic acid for 2-amino-2-deoxy-Dg-gluconic acid, the a-carbon of which has the configuration of
that in D-serine, and in which C-5, the highest numbered chiral centre, also has the D-configuration; (2) D8-mannosaminic acid
for 2-amino-2-deoxy-Dg-mannonic acid, the a-carbon of which has the configuration of that in L-serine, but in which C-5 has the
D configuration. The subscript g may be omitted unless confusion with the amino-acid use of the designations D and L is likely.
3AA-3.7. Use of meso

The prefix meso-, in lower case italic letters, is used to denote those amino acids or derivatives that, although they contain
chiral groups, are achiral, usually because of a plane of symmetry, e.g. meso-lanthionine.
3AA-3.8. Use of DL
A mixture of equimolar amounts of D and L compounds is termed racemic and is designated by the prefix DL (no comma), e.g.
(see 3AA-5).

DL-leucine. It may alternatively be designated by the prefix rac- (e.g. rac-leucine) or by the prefix ()3AA-4. CONFIGURATION AT CHIRAL CENTRES OTHER THAN THE a-CARBON

3AA-4.1. The Sequence Rule

The RS system (3AA-3.5) is preferred for designating configuration at centres other than a-C,e.g. (25,3R)-threonine. To
avoid using two different systems of designation in the same name, (25,45)-4-hydroxyproline may be used instead of (45)-4hydroxy-L-proline.

3AA-4.2 Carbohydrate Prefixes

The use of carbohydrate prefixes (e.g., D-erythrO) cited in the 1974 version of these recommendations [6] as an alternative
system for a-amino acids having two or more chiral centres is now discouraged.

3AA-4.3. Use of cis and trans

The amino acids 4-hydroxy-L-proline and 3-hydroxy-L-proline and analogous substituted prolines may also be named as
follows (cf. 3AA-3.2).

H2
N

H2

N
OH
COO

COO

OH
cis-4-hydroxy-L-proline

trans-4-hydroxy-L-proline

H2

H2

cis-4-hydroxy-D-proline

trans-4-hydroxy-D-proline

H2

H2

HO
COO

COO

OH
cis-3-hydroxy-L-proline

trans-3-hydroxy-L-proline

Nomenclature and symbolism for amino acids and peptides

603

The prefixes cis and trans refer to the relative positions of the hydroxyl and carboxyl groups in each compound.

Comment. The hydroxyprolines found in collagen are trans-4-hydroxyproline (predominantly) and trans-3-hydroxyproline.
The prefixes may be omitted when no ambiguity arises (cf. 3AA-3.3).
3AA-4.4. Use of'allo'

Amino acids with two chiral centres were named in the past by allotting a name to the first diastereoisomer to be discovered.
The second diastereoisomer, when found or synthesized, was then assigned the same name but with the prefix allo-. This method
A can be used only with trivial names (see 2.1) but not with semisystematic or systematic names. It is now recommended that allo

should be used only for alloisoleucine and allothreonine, as follows:

CH3

CH3

CH3

'CiCH3 CH CH

CH2 H

CH2 cH3

CH C,NH3

CO2 NH3

C02 H

L-isoleucine

D-isoleucine

CH3 OH

CH

CH3 H

C02 NH3

C02 H

L-threonine

D-threonine

CfiOH

CH2 CH3

,.),HNH3

c02-

L-alloisoleucine

CH3 H

COH
I

CNH3 CO2
CHNH3
L-allothreonine

CH3

CH2 H
NCfCH3

CO2 H
D-alloisoleucine

CH3 OH

CfIIH
I

C02- H
D-allothreonine

3AA-4.5. Designation of Centres with Unknown Configurations

A When absolute or relative configurations at one or more centres are not known, such designations as 'isomer A' and 'isomer
B' are frequently employed until the full configurational relationships are established.

If the configuration is known at one centre but not at a second, the RS system is used for the known centre, with a Greek

xi (),

meaning 'unknown configuration' for the other, e.g. (2S,5)-2-amino-5-hydroxyhexanoic acid (a single stereoisomer). If the

configuration at two centres is unknown, the may be used as in the example (2,5)-2-amino-5-hydroxyhexanoic acid. If a

racemate is to be designated, this is done by reference to its optical activity (3AA-5), e.g. ()-(2,5)-2-amino-5hydroxyhexanoic acid. If the relative configuration of two centres is known, but the absolute is unknown,'R*' and 'S*' may be

used, e.g. (2R*,5S*)2amino5hydroxyhexanoic acid.

3AA-4.6. Other Stereochemical Features
When other stereochemical elements are encountered, such as E/Z double-bond isomers, they are described according to the
provisions of Section E of the IUPAC rules for organic nomenclature [13].
3AA-5. OPTICAL ROTATION

If it is desired to indicate the direction of rotation of plane polarized light of specified wavelength in a specified solvent, this
can be done with a 'plus' or 'minus' sign in parenthesis (E-4.4 of reference [13]), e.g. (+)-6-hydroxytryptophan. This may be

particularly useful if the configuration at C-2 is not known, but it may also be done for emphasis, with or without a
configurational symbol D or L, when this configuration is known, e.g. (+ )-glutamic acid, or.( + )-L-glutamic acid. A racemic

amino acid (3AA-3.8) may be indicated by (), e.g.

Part

()-leucine.

1, Section B: NOMENCLATURE OF NON-PEPTIDE DERIVATIVES OF AMINO ACIDS

If an amino acid is substituted on a saturated carbon, it remains an amino acid. Its naming is therefore described in 3AA-2.
This section extends some of the procedures described there, and also covers modification of functional groups.
A number of special procedures are given below to allow names to be based on the trivial names of the a-amino acids, so that
they may indicate biochemical relationships. These procedures, which yield names such as N6-lysino (3AA-7), alanin-3-yl(3AA8), leucinamide (3AA-9.2), phenylalanylchloromethane (3AA-10.2), alaninol(3AA-10.3), etc., should not be extended to other
areas.
3AA-6. IONIZATION OF FUNCTIONAL GROUPS AND NAMING OF SALTS

The predominant form at pH 7 of a mono-amino-mono-carboxylic acid is RCH(NH)COO rather than RCH(NH2)

COOH. It is nevertheless often convenient to draw the latter conventional form (e.g. in Table 1) and to name alanine as 2-

604

IUPAC-IUB JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE

aminopropanoic acid

rather than as 2-ammoniopropanoate. This is particularly so for representing the isoelectric form of amino
acids that contain other ionizing groups. A solution of lysine, for example, would contain appreciable amounts of both NH

[CH2]4-CH(NH2)-C00 and NH2-[CH2]4-CH(NH)-COO

When it is desirable to mention or stress the ionic nature ofan amino acid, the three kinds ofions possible for a mono-aminomono-carboxylic compound may be indicated as follows:
NHCH2COO

glycine zwitterion (or dipolar ion, or amphion);

NHCH2COOH

glycinium, or glycine cation;

NH2CH2--C00

glycinate, or glycine anion.

In indicating an anion the ending 'ate' replaces 'ic acid' or the final 'e' of the trivial name, or is added to the name tryptophan.
Further forms are required for amino acids that contain ionizing side chains. The singly charged anions of aspartic and
glutamic acids (strictly each has two negative and one positive charge, but this nomenclature refers to net charge) may be
distinguished from the doubly charged anions by placing the charge after the name, or by stating the number ofneutralizing ions.
Thus the form of glutamate (glutamate refers to glutamic acid ; glutaminate is the anion from glutamine) with a charge of minus
one, OOCCH2CH2CH(NH)COO , may be called glutamate(1-), glutamic acid monoanion, or hydrogen glutamate, and
its sodium salt may be called sodium glutamate(1-), sodium hydrogen glutamate, or monosodium glutamate. The corresponding
terms for the dianion, 00CCH2CH2CH(NH2)C00, include glutamate(2-), glutamic-acid dianion, and disodium
glutamate. Unqualified, the word glutamate systematically means the dianion ; hence the usage 'sodium hydrogen glutamate' ; in
normal use, however, it means the ion ofnet charge -1, since this is the form that predominates in neutral solution, and it is used in
this way in, for example, 'a glutamate-dependent reaction' and 'glutamate dehydrogenase'.
Similarly, forms such as lysinium(1 + )or lysine monocation may be used for the ion ofunit net charge derived from lysine. Its
salts may be indicated by adding the name of the anion to the lysinium form, e.g. lysinium(1 + ) chloride, or by naming it lysine
monohydrochloride. The fully protonated form is the lysine dication or lysinium(2+).
3AA-7. AMINO ACIDS SUBSTITUTED ON NITROGEN

Since N-2 is the atom most easily modified in many amino acids, the locant can often be omitted without ambiguity, e.g.
acetylglycine for N-acetylglycine.
It is sometimes convenient to use the name ofa group derived by loss ofhydrogen from a nitrogen atom ofan amino acid as a
prefix in forming another name. Such prefixes are formed by substituting 'o' for the terminal 'e' in those names that end in 'e' (by
analogy with amineamino); e.g. alanino, valino. Tryptophan adds the 'o' directly, and the two dicarboxylic acids become
asparto and glutamo. Where there is more than one nitrogen atom in the amino acid, a locant of the form N' must precede the
group name. e.g. N6-lysino, N"-arginino, N5-glutamino, N'-histidino.
3AA-8. SIDE-CHAIN MODIFICATIONS (excluding modifications of carboxyl or nitrogen)
Most modified amino acids can be named according to 3AA-2, e.g. S-(carboxymethyl)-L-cysteine. Groups formed by loss of
hydrogen atoms from carbon, sulfur or oxygen atoms (excluding the carboxylic oxygen atoms, which are dealt with under 3AA9) are named by substituting '-x-yl' for the terminal 'e' of the trivial name, where 'x' is the locant of the atom from which the

hydrogen atom has been lost, e.g. cystein-S-yl, threonin-03-yl, alanin-3-yl, or by adding '-x-yl' to aspartic, glutamic and
tryptophan, e.g. aspartic-2-yl, tryptophan-2-yl (see 3AA-2.2.3).
Comment. tryptophan-1-yl should be named 1-tryptophano according to 3AA-7.
A common side-chain modification is the oxidation of cysteine to yield cystine (formula in Appendix). Hydrogen atoms are
removed from the SH groups of two molecules, which are joined by an SS bond. The term 'half cystine' refers to each half. It
occurs seldom in naming compounds, since half a cystine molecule is a substituted cysteine and is named as such. In stating
amount of substance, however, any specified entity may be used, so moles or numbers of residues of half cystine may usefully be

compared with these quantities of other amino acids in stating protein composition.
3AA-9. ESTERS AND AMIDES OF THE CARBOXYL GROUP

3AA-9.l. Esters
Esters are named with the anion name (3AA-6), e.g. methyl prolinate, methyl cysteinate, or from the amino acid, e.g. proline
methyl ester, cysteine methyl ester.
3AA-9.2. Amides, Anilides and Analogous Derivatives (H2NCHRCONHR')

In amides, anilides and analogous derivatives of a-amino acids the hydroxyl group of the carboxyl has been replaced by an
amino, anilino, or analogous group. They may be named by replacing the final 'e' of the trivial name of the amino acid by the
word 'amide', 'anilide', etc., e.g. glycinamide, leucinamide, argininanilide. Alternatively, these compounds may be described as
glycine amide, leucine amide, etc.
Note that the 4-amide of aspartic acid and the 5-amide of glutamic acid have specific trivial names, asparagine and glutamine.
Their 1-amides are named aspartic 1-amide and glutamic 1 -amide, or isoasparagine and isoglutamine.

Nomenclature and symbolism for amino acids and peptides

3AA-9.3.

605

Acyl Groups

The acyl group ofan a-amino-mono-carboxylic acid is a structure that lacks the hydroxyl group ofthe carboxyl (H2NCHR
CO). The names ofsuch groups are formed by replacing the ending 'me' (or 'an' in tryptophan) by 'yl' (C-421 ofreference [14]),
e.g. alanyl, arginyl, tryptophyl. 'Cysteinyl' is used instead of'cysteyl', because ofpotential confusion with the group from cysteic

acid. 'Cystyl' is the diacyl group of cystine, and 'haif-cystyl' is the acyl group of cysteine lacking also the H of its SH group.
The monoacyl groups derived from aspartic acid, HOOCCH2CH(NH2)CO and CO-CH2CH(NH2)COOH, are

designated a-aspartyl (or aspart-1-yl) and /3-aspartyl (or aspart-4-yl) respectively; the corresponding groups derived from
glutamic acid are a-glutamyl (or glutam-1-yl) and y-glutamyl (or glutam-5-yl) (C-421.3 of reference [14]). The diacyl groups
formed from the dicarboxylic amino acids are aspartoyl and glutamoyl. The acyl groups derived from asparagine and glutamine
are termed asparaginyl and glutaminyl respectively.
3AA-10. CARBOXYL GROUP MODIFICATIONS OTHER THAN ESTER AND AMIDE FORMATION

3AA-10.1. Removal of the Carboxyl Group

Several decarboxylated amino acids have trivial names terminated with 'amine' : tyramine, histamine, cysteamine,
tryptamine, methioninamine. Similarly cystine (see Appendix) forms cystamine.
3AA-10.2. Ketones

If the hydroxyl group of the 1-carboxyl is replaced by an alkyl group, the name of the ketone formed can use the name of the
amino acid by naming the compound as a substituted hydrocarbon, e.g. phenylalanyichioromethane for C6H5CH2CH(NH2)-COCH2C1, 3-amino-1-chloro-4-phenylbutan-2-one (see also 3AA-18.2). This type of name is based on the trivial names of
amino acids (or peptides), so does not place the substituents ofmethane in alphabetical order (as systematic nomenclature does),
but places 'chloromethane' at the end because this indicates C-terminal modification (see 3AA-1 3.1). The practice ofusing names

such as 'phenylalanine chioromethyl ketone' is discouraged, because they erroneously specify the carbonyl group twice.
3AA-10.3. Aldehydes and Alcohols
Aldehydes and alcohols obtained by successive stages of reduction of the carboxyl group of a-amino acids are named by
replacing the final 'e' of a trivial name ending in 'me' (or the 'ic acid' of aspartic and glutamic acids) with the endings 'al' and 'ol'
respectively.
Examples. RCH(NH2)CHO : alaninal, leucinal, lysinal, serinal, aspart-1-al, glutaminal. RCH(NH2)CH2OH: alaninol,

leucinol, lysinol, serinol, aspart-1-ol, glutaminol. The aldehyde and alcohol derivatives of tryptophan take the names
tryptophanal and tryptophanol. The name glycinol is little used, because the systematic name 2-aminoethanol is short, and this
already has the trivial name ethanolamine [19].
Note. The derivative of lysine in which the CH2NH2 group is replaced by CHO has the trivial name allysine (see
Appendix).

Part 1, Section C: PEPTIDE NOMENCLATURE

3AA-1 1. DEFINITION OF PEPTIDES

A peptide is any compound produced by amide formation between a carboxyl group of one amino acid and an amino group
of another. The amide bonds in peptides may be called peptide bonds. The word peptide usually applies to compounds whose
amide bonds are formed between C-I of one amino acid and N-2 of another (sometimes called eupeptide bonds), but it includes
compounds with residues linked by other amide bonds (sometimes called isopeptide bonds). Peptides with fewer than about 10
20 residues may also be called oligopeptides; those with more, polypeptides. Polypeptides of specific sequence of more than about
50 residues are usually known as proteins, but authors differ greatly on where they start using this term.
3AA-12. AMINO-ACID RESIDUES

3AA-12.l. Definitions of Residues

When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of
each amino acid is called an amino-acid residue. a-Amino-acid residues are therefore structures that lack a hydrogen atom of
the amino group (NHCHR--COOH), or the hydroxyl moiety of the carboxyl group (NH2CHRCO), or both (NHCHR

CO); all units of a peptide chain are therefore amino-acid residues. (Residues of amino acids that contain two amino groups or

two carboxyl groups may be joined by isopeptide bonds, and so may not have the formulas shown.)
The residue in a peptide that has an amino group that is free, or at least not acylated by another amino-acid residue (it may, for
example, be acetylated or formylated), is called N-terminal; it is at the N-terminus. The residue that has a free carboxyl group, or
at least does not acylate another amino-acid residue, (it may, for example, acylate ammonia to give NHCHRCONH2), is
called C-terminal. If the amino group of the N-terminal residue is free, the residue may be named as an acyl group under 3AA-9.3;

indeed any internal residue is an N-substituted amino-acyl group.

Residues are named from the trivial name of the amino acid, omitting the word 'acid' from aspartic acid and glutamic acid.
Examples: glycine residue, lysine residue, glutamic residue.

IUPAC-IUB JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE

606

3AA-12.2. Ionized Forms of Residues

When it is desirable to mention or emphasize the particular ionic form of a residue, this may be done as follows
Name of residue

Protonatedform
argininium residue

arginine residue
histidine residue
lysine residue
aspartic residue
cysteine residue
glutamic residue
tyrosine residue

histidinium residue
lysinium residue
aspartic (acid) residue
cysteine (acid) residue
glutamic (acid) residue
tyrosine (acid) residue

Deprotonated form
arginine (base) residue
histidine (base) residue
lysine (base) residue
aspartate residue
cysteinate residue
glutamate residue
tyrosinate residue

This system cannot easily be applied to N- or C-terminal residues.

3AA-13. THE NAMING OF PEPTIDES
3AA-13. 1 . Construction of Names

To name peptides, the names ofacyl groups ending in 'yl' (3AA-9.3) are used. Thus ifthe amino acids glycine, NHCH2-COO-, and alanine, NHCH(CH3)COO, condense so that glycine acylates alanine, the dipeptide formed, NHCH2CO
NHCH(CH3)C00, is named glycylalanine. Ifthey condense in the reverse order, the product, NHCH(CH3)CONH
CH2C00 , is named alanylglycine. Higher peptides are named similarly, e.g. alanylleucyltryptophan. Thus the name of the
peptide begins with the name ofthe acyl group representing the N-terminal residue, and this is followed in order by the names of
the acyl groups representing the internal residues. Only the C-terminal residue is represented by the name ofthe amino acid, and
this ends the name ofthe peptide. Formulas should normally be written in the same order, with the N-terminal residue on the left,

and the C-terminal on the right, e.g.

NH2-CH(COOH)-[CH2]2-CO-NH-CH(CH2SH)--CO-NH-CH2-COOH
glutathione, y-glutamylcysteinylglycine

A multiplicative affix (p. 5 of reference [14]) placed before 'peptide' gives the total number of residues in the peptide, e.g.
A hexapeptide. Since the higher affixes are not well known, they may be replaced by numerals, e.g. a 22-peptide.
Higher oligopeptides and polypeptides of biological origin often have trivial names ; their sequences are usually described
more conveniently by symbols (3AA-14 to 3AA-19 below) than by constructing long names.
3AA-13.2. Use of Prefixes in Peptide Names
Configurational prefixes (3AA-3) are placed immediately before the trivial names of the residues they refer to. The prefixes
are set off from the names before and after them with hyphens. Examples: L-alanyl-L-leucine; L-alanyl-D-leucrne; glycyl-Lalanine; L-alanylglycine; L-leucyl-L-phenylalanyl-L-leucylglycine; L-alanylglycyl-L-leucine.
A
The mixture of diastereoisomers formed by condensations between DL-amino acids will contain unspecified proportions of
each pair of enantiomers. Names such as DL-alanyl-DL-leucine have been used in the past, but they are misleading because they
contradict the accepted meaning of the prefix DL as signifying a racemate; here the racemate of L-alanyl-L-leucme and D-alanylD-leucine (which may be designated as rac-L-alanyl-L-leucine) is mixed in unspecified proportions with the racemate of L-alanylD-leucine and D-alanyl-L-leucine (which may similarly be designated as rac-L-alanyl-D-Ieucine). This is better indicated by the
name ambo-alanyl-ambo-leucine (item 12c of reference [20]).
A mixture of L-alanyl-L-alanyl-L-alanine and L-alanyl-D-alanyl-L-alanme may likewise be called L-alanyl-ambo-alanyl-Lalanine.
3AA-13.3. Name of Simple Polymers of ct-Amino Acids

Simple polymers of amino acids may, if preferred, be named with prefixes to indicate the number of amino-acid residues
present, e.g. tetraglycine. Mixtures of polymers with varying numbers of residues may be given names like oligoglycine,
polyglycine, poly(L-lysine), etc. [21].

3AA-13.4. Numbering of Peptide Atoms

The atoms of a peptide may need to be numbered as locants for substitution or isotopic replacement. Often no more
numbering is required than that of atoms within a residue (see 3AA-2.2), e.g. alanyl-3-chloroalanylalanine. It may sometimes be

convenient to indicate substitution of the peptide as a whole. This may be done by adding the residue number, obtained by
A numbering residues from the N-terminus, after the atom number, and separated from it by a point. The above compound may
therefore be called 3.2-chloro(alanylalanylalanine). Thus the atom C-3.2 is C-3 of the second residue of the peptide. Example:
Alanylthreonylglycylaspartylglycine 4.4-3.2-lactone for the compound that can be represented (3AA-16, -17 and -19 below) as
Ala-Tfir-Gly-Ap-Gly.
Such numbering is especially useful for peptides with trivial names (see 3AA-22.5), e.g. N5 4-methyloxytocin would indicate a

methyl substituent on N-5 of the glutamine residue at position 4 of oxytocin. If the peptide name that follows a substituent

Nomenclature and symbolism for amino acids and peptides

indicated in

607

this way is constructed residue by residue, it must be placed in parentheses to show that the numbering applies to the

peptide as a whole, rather than to the first residue.

3AA-13.5. Prefixes Formedfrom Peptide Names
A When it is necessary to treat a peptide as a substituent, the point ofattachment is specified by the suffix 'yl' (see 3AA-8) with
the appropriate locant. Ifthe group formed from the peptide is not the acyl group derived by removing hydroxyl from C-i of the
C-terminal residue, the position at which hydrogen (or hydroxyl from a side-chain carboxyl group) is removed should be
indicated by a locant before the 'yl' ; if the sequence of the peptide is given in full, it should be placed in parentheses to avoid
implying that the group is formed by removing H or OH from the C-terminal residue. Examples:
(1) Leukotriene D, or (7E,9E,liZ,14Z)-(5S,6R)-6-[(cysteinylglycin)-S-yl]-hydroxyicosa-7,9,i i,14-tetraenoic acid;

(2) Leukotriene C, or (7E,9E,11Z,14Z)-(5S,6R)-6-(glutathion-S-yl)-5-hydroxyicosa-7,9,ii,i4-tetraenoic acid, or (7E,9E,

1 iZ,14Z)-(5S,6R)-6-[(y-glutamylcysteinylglycin)-S-yl]-5-hydroxyicosa-7,9,li,i4-tetraenoic acid;

(3) (2S)-2-O-[(serylalanylserin)-3.2-yl]lactic acid, or (2S)-2-[(serylserylserin)-032-yl}propanoic acid, or 032-[(1S)-icarboxyethyl](serylserylserine).

If the locant before 'yl' indicates the carbon of a carboxyl group, the prefix indicates the acyl group formed by removing
hydroxyl from this atom. Example : 4-O-[(glutamylglutamylglutamic acid)-5.2-yl]-D-gluconic acid.

3AA-i3.6. Conformation of Polypeptide Chains

Abbreviations and symbols for describing the conformation of peptide chains have been published separately [i6].

Part 2. Symbolism
Part 2, Section A: THE THREE-LETTER SYSTEM (a revision and updating of [10])
3AA-14. GENERAL CONSIDERATIONS ON THREE-LETTER SYMBOLS

14.1. The symbol chosen for an amino acid (Table 1) is derived from its trivial name, and is usually the first three letters of this
name. It is written as one capital letter followed by two lower-case letters, e.g. Gln (not GLN or gln), regardless of its position in a
sentence or structure. If any other convention is used in representing residues, e.g. to emphasize homology, this should be stated
clearly whenever it is used. When the symbol is used for a purpose other than representing an amino-acid residue, e.g. to designate

a genetic factor, three lower-case italic letters may be used, e.g. gin.
14.2. The main use of the symbols is in representing amino-acid sequences. Inasmuch as the symbols by themselves represent
the unsubstituted amino acids, they are modified (3AA-1 6) by hyphens to represent residues. We do not recommend use of the
symbols to represent free amino acids in textual material, but such use may be desirable in tables, diagrams or figures. It may also
be convenient to use them for indicating residue numbers, e.g. Tyr-1 10 for tyrosine residue 110. For substituents, supplementary
symbols are used (3AA-17 and -18).
14.3. A symbol may represent either the name or the formula of a compound.
14.4. Heteroatoms of amino-acid residues (e.g. 0-3 serine, N-6 of lysine) do not explicitly appear in the symbol, as it
represents the whole molecule including them (but see 3AA-17.4).
14.5. Amino-acid symbols denote the L configuration of chiral amino acids unless otherwise indicated by the presence of D or
DL before the symbol and separated from it with a hyphen (see also 3AA-19.2). L may similarly be inserted for emphasis.
14.6. Structural formulas may be used together with symbols to make complicated features or reactions clear (for examples
see 3AA-17.4).
3AA-i5. SYMBOLS FOR AMINO ACIDS

3AA-i5.i. Symbols for Common Amino Acids

The symbols for the amino acids that are coded for by mRNA are listed in column 2 of Table 1.
3AA-i5.2. Symbols for Less Common Peptide Constituents
Symbols for less common amino acids should be defined in each publication in which they appear. The following principles
and notations are recommended.

15.2.1. Hydroxyamino Acids

The symbol 5Hyl is recommended for 5-hydroxylysine, and 4Hyp for 4-hydroxyproline (the numbers may be omitted,
especially when limiting the symbols to three letters helps alignment of sequences, provided that the position of substitution is
made clear in the text). Similarly 3Hyp would represent 3-hydroxyproline. Alternatively, symbols may be formed as shown in
3AA-i7.3 below for substituted residues, so that 4-hydroxyproline may be written as:
OH
Pro(4-OH)

41
or Pro

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608

15.2.2.

Alloisoleucine and Allothreonine

Alloisoleucine and allothreonine (3AA-4.4) may be symbolized by aIle and aThr respectively.

15.2.3. 'Nor' Amino Acids

Since 'nor' in 'norvaline' and 'norleucine' is not used in its systematic sense ofdenoting a lower homologue, but to change the

trivial name of a branched-chain compound to designate a straight-chain compound, its use for amino acids should be
A progressively abandoned (3AA-2.4), along with the earlier symbols Nva and Nie. Appropriate symbols for these compounds, 2aminovaleric and 2-aminohexanoic acids, based on symbols proposed for the unsubstituted acids [19], are Avi and Ahx (see also
3AA-15.2.5).

15.2.4. 'Homo' Amino Acids

The prefix 'homo', used in the sense of a higher homologue, is commonly used for two amino acids (3AA-2.3). They are
symbolized as follows:
Homoserine

Hse

Homocysteine

Hcy

15.2.5. Higher Unbranched Amino Acids

The functional prefix 'amino' is included in the symbol as the letter 'A' and 'diamino' as 'A2'. The trivial name of the parent
acid is abbreviated to two letters, based, when possible, on the symbols for lipid nomenclature [19]. Unless otherwise indicated,
single groups are on C-2, two amino groups are in the 2 and terminal positions for monocarboxylic acids, and each is geminal with
a carboxyl group for dicarboxylic acids. The location of amino groups other than these is shown by appropriate prefixes.

A
A

A
A

Examples

Symbol

f3-Alanine (3-aminopropanoic acid)

2-Aminobutyric acid (2-aminobutanoic acid)
2-Aminovaleric acid (2-aminopentanoic acid)
2-Aminohexanoic acid
6-Aminohexanoic acid

f3Ala

2-Aminoadipic acid (2-aminohexanedioic acid)

3-Aminoadipic acid (3-aminohexanedioic acid)
2-Aminopimelic acid (2-aminoheptanedioic acid)
2,3-Diaminopropionic acid (2,3-diaminopropanoic acid)
2,4-Diaminobutyric acid (2,4-diaminobutanoic acid)
Ornithine (2,5-diaminovaleric acid, 2,5-diaminopentanoic acid)
2,6-Diaminopimelic acid (2,6-diaminoheptanedioic acid)

Aad

Note

Abu

Ape
Ahx
cAhx
/3Aad

Apm

A2pr or Dpr
A2bu or Dab
Orn
A2pm or Dpm

ii, iii, iv
ii

ii, iii

Notes

i) This symbol is recommended in place of the previous eAcp, in which 'cp' stood for caproic, which may be confused with capric and
caprylic.
ii) The previous edition of these recommendations (10) discouraged abbreviations starting 'D' for 'di' or 'T' for 'tn' or 'tetra'; because these
letters were overused. We concur in preferring subscripts when these can be applied to well-known symbols, so that Me2SO is preferable to
DMSO, Me3Si- to TMS-, and H4 to TH. Nevertheless we are not convinced that 'A2' easily suggests 'diamino', so alternative symbols are
presented.
iii) 'Dap' should not be used as a symbol, since it could be construed to mean either diaminopropanoic acid or diaminopimelic acid.
iv) 2,3-Diaminopropanoic acid can be regarded as 3-aminoalanine, and so may be symbolized by 'side-chain substitution' (3AA-17.3 below)
as Ala(NH2) or Ala, but users should beware of the possibility that the former may be confused with Ala-NH2 (3AA-17.1), the symbol for
alaninamide.
I
NH2

15.2.6.

Carboxylated and Oxidized Amino Acids

Symbols are recommended for two amino acids that have an additional acidic group and may occur in polypeptide sequences.
They are:
4-Carboxyglutamic acid Gla
Cysteic acid

Cya

Nomenclature and symbolism for amino acids and peptides

15.2.7.

Non-Amino-Acid Residues in Peptides

Symbols for sugar residues (e.g. Gic, Gal) have been proposed [22], as have ones for nucleoside residues (e.g. Ado, Cyd) [23],

and these may be combined with amino-acid symbols to represent glycopeptides, etc. These symbols include [221 Neu for
neuraminic acid, Neu5Ac for N-acetyl neuraminic acid, and Mur for muramic acid. Depsipeptides (3AA-19.6) contain hydroxyacid residues; when symbols are used for these they should be defined.
3AA-16. SYMBOLISM OF AMINO-ACID RESIDUES

3AA-16.1. General Principles for Symbolizing Residues

The peptide glycylglycylglycine is symbolized as Gly-Gly-Gly. This involves modifying the symbol Gly for glycine, NH2
CH2COOH, by adding hyphens to it, in three ways:

i) Gly-= NH2-CH2-CO-ii) -Gly =-NH-CH2-COOH

iii) -Gly- = -NH-CH2-CO-

(normally as NHCH2-CO-)

(normally as -NH-CH2-COO)

Thus the hyphen, which represents the peptide bond, removes OH from the 1 -carboxyl group of the amino acid (written in the
conventional un-ionized form) when it is placed on the right of the symbol (i), and removes H from the 2-amino group of the
amino acid when it is placed on the left of the symbol (ii); both modifications can apply to one symbol (iii).
Thus the peptide Gly-Glu (without hyphens at its ends) is distinguished from the sequence -Gly-Glu- (with hyphens at its
ends).
3AA-16.2. Lack of Hydrogen on the 2-Amino Group
A hyphen on the left of the symbol signifies removal of a hydrogen atom from the 2-amino group, as well as representing the
bond formed by the group thus produced. If it should prove necessary to draw a bond to N-2 on the right of the symbol (e.g. in a
cyclic peptide, 3AA-19.4 below), then the hyphen must be replaced by an arrow, which points from CO to NH within the peptide

bond.
If both atoms on N-2 are replaced, two lines can be drawn on the left of the symbol, e.g.

)Ala or -i--Ala for )N-CH(CH3)-COOH

3AA-16.3. Lack of Hydroxyl on the 1-Carboxyl Group
A hyphen on the right of the symbol signifies removal of hydroxyl from the 1-carboxyl group as well as representing the bond
formed by the group produced. If it is not possible to draw this bond on the right of the symbol, as in a cyclic peptide (3AA-19.4)

then the hyphen must be replaced by an arrow, which has the same effect.
3AA-16.4. Removal of Groups from Side Chains

16.4.1. Monocarboxylic Acids

A vertical line drawn above or below the symbol for a monocarboxylic amino acid represents removal of hydrogen from the
side chain so that a radical is formed. Replacement of this hydrogen by a substituent is treated in 3AA-17.2 below. Unless
indicated by a locant placed beside the line, the hydrogen is assumed to be removed from a heteroatom in the residue. Examples:

0
CH2

Ser

means NH-CH-COO
NH
[CH2]4

Lys

means NH-CH-COO
CH-CH2-NH
[CH2]2

J5
Lys

means NH-CH-COO

609

610

IUPAC-IUB JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE

Notes. (a) H is removed from N-w rather than N-5 of arginine unless otherwise indicated; (b) a locant, ir or x(3AA-2.2.4), is
always required for histidine.

16.4.2. Dicarboxylic acids

A vertical line drawn above or below either of the symbols Asp and Glu represents removal of OH from the side-chain
carboxyl group, as well as representing a bond to a substituent. If a hydrogen has to be removed from a saturated carbon of the

side chain, then a vertical line may be used, but it must be accompanied by a locant. Examples:
CO
CH2

Asp

means NHCH-COO
CHC00

13

Asp

means NH-CH-COO

3AA-16.5. Cyclic Derivatives of Amino Acids

Combination of horizontal lines, indicating removal of H from N-2(3AA-16.1, 3AA-16.2)or OH from C-I (3AA-16.1, 3AA16.3), with the vertical lines that indicate removal of side-chain atoms (3AA-16.4) allows formation of symbols for 5-oxoproline
(systematically 5-oxopyrrolidine-2-carboxylic acid, also known as pyroglutamic acid or pyrrolidonecarboxylic acid) and for

homoserine lactone, as follows:

OC-[CH2]2

LG1U or <Gluor Glp-

HNCH-CO[CH2]2-O

-NH-CH---CO

-Hse-1 or -Hse>
or Hsl

3AA-17. SUBSTITUTED AMINO ACIDS

3AA-17.1. Substitutions in the 2-Amino and 1-Carboxyl Groups

This follows logically from 3AA-16.1, 3AA-16.2 and 3AA-16.3 by using symbols for atoms or groups to represent the
substituents. Examples (see also 3AA-18.2):
Ac-Gly
Gly-OEt
Ac-Lys
Ser-OMe
Ac-Glu-OEt
Glu-NH2
Asp-OMe

N-Acetylglycine
Glycine ethyl ester
N2-Acetyllysine
Serine methyl ester
o1-Ethyl N-acetylglutamate
Isoglutamine

01-Methyl hydrogen aspartate

A second substituent on N-2, when the first is shown with a line as above, may be represented with a second line to the left of the

symbol for the substituted residue: Xaa. It may be convenient to print this as a vertical line joining the first: 'Xaa.
Example: alanyl-N-methylvaline may be represented
Me

Me

Me
I

/
Ala

Val

or AlaVal or Ala1Val

3AA-17.2. Substitutions on Side-Chain Functional Groups

Side-chain substituents may be portrayed above or below the amino-acid symbol (3AA-16.4) or by placing the symbol for the

A substituent in parentheses immediately after the amino-acid symbol. When the symbol for a substituent, such as an
oligosaccharide, has a hyphen on its right-hand side to indicate the bond to the amino acid [22], then this symbol should be placed

in parentheses before the amino-acid symbol rather than after it, e.g. -(Galfll-4Xyl/31-)Ser- [22].
Symbols within parentheses written on one line should normally be used only in textual material and when the symbol for the
substituent is short; otherwise the two-line symbols containing a vertical line will be clearer. Note that the substituents

611

Nomenclature and symbolism for amino acids and peptides

represented replace hydrogen except when the amino acid is aspartic acid or glutamic acid, when they replace the OH of the
carboxyl group unless otherwise specified (3AA-16.4.2).
If a locant is required, it is placed beside the vertical line that represents side-chain substitution, or is joined to the substituent
symbol within the parentheses by a hyphen.

Notes

Examples

Symbols
OMe

04-Methyl hydrogen aspartate (fl-methyl aspartate)

Asp or Asp or Asp(OMe)

OMe

OEt
05-Ethyl hydrogen N-acetylglutamate

AcGlu or AcGlu(OEt)

Ac
N6-Acetyllysine

Lys or Lys(Ac)
Ac

03-Acetylserine

Ser or Ser(Ac)

04-Sulfotyrosine (tyrosine 04-sulfate)

Tyr or Tyr(SO3H)
Et

5-Ethylcysteine

Cys or Cys(Et)
OH

SO3H

A 3-Sulfenoalanine

ii

Cys or Cys(OH)
SO3H

A S-Sulfocysteine (S-cysteinesulfonic acid)

ii, iii

Cys or Cys(SO3H)

CN
5-Cyanocysteine

Cys or Cys(CN)

II

Cys
I

Cystine

Cys or Cys Cys (not Cys-Cys)

D-Cystine

D-Cys D-Cys

meso-Cystine

L-Cys D-Cys or D-Cys L-Cys

A Methionine S-oxide (methionine oxide)

A Methionine S,S-dioxide (methionine dioxide)

Met or MetO
02
Met or MetO2

I
ii, iv

ii, iv

P
Phosphoserine (03-phosphonoserine)

Ser or Ser(P)

Me
His or His(t-Me)
N'-Methylhistidine (telemethylhistidine, see 3AA-2.2.4)
Notes
i) Asp-OMe represents the O'-methyl ester of aspartic acid (C-i modification by 3AA-16.3), whereas Asp(OMe) represents the 04-methyl
ester (side-chain modification by 3AA-i6.4.2).
ii) Names based on cysteine and symbols based on Cys already indicate sulfur in the molecule, and similarly with methionine and Met.
Indication of modification of this sulfur should not suggest the addition of further sulfur. Hence calling 3-sulfenoalanine by the name
cysteinesulfenic acid, 3-sulfinoalanine by the name cysteinesulfinic acid, methionine S-oxide by the name methionine sulfoxide, and methionine
5,5-dioxide by the name methionine sulfone may be confusing and is not recommended.
iii) Care should be taken with this symbol because readers who fail to realize that the symbol Cys contains the sulfur may confuse it with
cysteic acid, now symbolized Cya (3AA-i 5.2.6). The earlier [10] symbol Cys for cysteic acid has the disadvantage that the vertical line in it does

not represent a single bond.

03H
iv) The vertical lines or parentheses previously [10] in the symbols for MetO and MetO2 are now omitted, because they wrongly implied
removal of hydrogen.
v) P represents P03H2 [24].

IUPAC-IUB JOINT CONNISSION ON BIOCHEMICAL NOMENCLATURE

612

3AA-17.3.

Substitution on Side-Chain Skeleton

This may use the same convention as 3AA-17.2, with the addition of locant numerals where necessary (see 3AA-16.4), e.g.
COOH
4j

Glu as an alternative to Gla (3AA-15.2.6) if it is desired to

4-Carboxyglutamic acid

emphasize carboxylation
NH2

Ala or Ala(NH2)

2,3-Diaminopropanoic acid
(3-aminoalanine, see 3AA-15.2.5)
3,5-Diiodotyrosine

Tyr(12) or Tyr(3,5-12) if the context does not imply the locants

NO2

3-Nitrotyrosine

Tyr

3AA-17.4. The Use of Symbols in Representing Reactions of Side-Chains

The symbols are designed primarily to indicate sequence, and care must be taken to avoid confusion when they are adapted to
other uses.
Although the conversion of a cysteine residue in a protein into an S-carboxymethylcysteine can be adequately represented as
Cys- -Cys(CH2-COOH)-

writers may wish to show the sulfur atom in order to indicate the chemistry of the reaction. Although it would be perfectly
legitimate to write
-Ala(SH)- + -Ala(S-CH2-COOH)-

this would be confusing since the residue is thought of as cysteine rather than as modified alanine.
We therefore recommend putting the residue symbol into quotation marks if one of its groups is to be depicted separately (or,
alternatively, using the symbol Raa). Hence the thiol group of a cysteine residue may be shown as:

SH

SH
'Cys' or

Terminal amino and carboxyl groups can be shown similarly, e.g. H2N'Ala' to show explicitly the amino group present in Ala(in contrast with --AlaNH2 which shows the amide of C-terminal alanine). This convention allows mechanisms to be drawn

out, e.g.
cO2-

CO2-

CH- p

'Cys'

with the

SCH2

'Cys'

quotation marks to alert readers to the fact that the symbol here does not include the sulfur atom. Sequences may also be

shown, so that the acylation of a serine proteinase could be drawn as:

R-CO-X
GlyAsp--'Ser'Gly

R-CO + HX
GlyAsp'Ser'GIy

When this convention is used it should be described.

3AA-17.5. Mody'Ied Residue in Natural Peptides

If an unusual residue is to be symbolized within a particular context, it may be helpful to modify (e.g. with an asterisk) the
symbol for the ribosomally incorporated residue, e.g. Ser* for 2-aminopropenoic acid (formed within a peptide chain by
dehydration of a serine residue). Such an asterisk may be placed above the residue rather than after it to allow alignment with
other 3-letter symbols. Symbols modified in this way should be defined when used.
3AA-17.6. Lack of Substitution
If it is desired to emphasize lack of substitution, H or OH may be added to the hyphen or vertical line that represents removal

of one of these groups. Thus H-Ala may be contrasted with Ac-Ala, and Ala-OH with Ala-OMe.

613

Nomenclature and symbolism for amino acids and peptides

3AA-18. SYMBOLS FOR SUBSTITUENTS

3AA-18.1. Use of Symbols

Groups substituted for hydrogen or hydroxyl may be indicated by their formulas or by symbols or by combination of
both, e.g.
Benzoylglycine (hippuric acid)

PhCO-Gly or C6H5CO-Gly

Note: the symbol Bz is often used for benzoyl in organic chemistry, and Bzl for benzyl, but because these symbols are so
similar, the alternative PhCO and PhCH2 are preferable.
Glycine methyl ester
Trifluoroacetylglycine

GlyOCH3 or GlyOMe
(Table 3, Note ii)
CF3COGly

Suggestions for symbols to designate substituent (or protecting) groups common in peptide and protein chemistry are given in

Tables 2, 3 & 4.

Table 2. Nitrogen substituents (protecting groups) of the urethane type

Benzyloxycarbonyl2-(p-Biphenylyl)isopropyloxycarbonyl[strictly 1-(biphenyl-4-yl)-1 -methylethoxycarbonyl-]
p-Bromobenzyloxycarbonylt-Butoxycarbonyla,a-Dimethyl-3,5-dimethoxybenzyloxycarbonylFluoren-9-ylmethoxycarbonyl
p-Methoxybenzyloxycarbonyl
p-Nitrobenzyloxycarbonyl
p-Phenylazobenzyloxycarbonyl

Z- or CbzBpoc-

Z(Br)Boc- or ButOCO- or t-BuOCO- or Me3COCO

Ddz

Fmoc
Z(OMe)
Z(NO2)
Pz

Table 3. Non-urethane substituents for nitrogen, oxygen or sulfur

Acetamidomethyl

Acm

Acetyl

Ac-

Benzoyl

Benzyl

(C6H5CO)
(C6H5CH2)

Carbamoyl
(3-Carboxy-4-nitrophenyl)thio
3-Carboxypropanoyl (HOOCCH2CH2CO)
Dansyl, 5-(dimethylamino)naphth-1-ylsulfonyl
2,4-Dinitrophenyl
Formyl
4-Iodophenylsulfonyl (pipsyl)

PhCO (or Bz; see note in 3AA-18.1)

PhCH2 (or Bzl; see note in 3AA-18.1)
NH2CO (preferred to Cbm)
Nbs (see 3AA-18.2)
Suc (see Note i)

Dns

Dnp or N2ph (see Note ii)

HCO or For-- (see Note iii)
'Ps

or Mal-z(C--404.l of [14])

Maleoyl- (-OC-CH = CH-CO-)

Maleyl- (HOOC-CH = CH-CO-)

Mal--

2-Nitrophenylthio
Phenyl(thiocarbamoyl)
Phthaloyl
Phthalyl (o-carboxybenzoyl)

NpS (Nps often used)

Succinyl (OCCH2CH2CO)
Tosyl

Suc or Suc <

Trifluoroacetyl
Trityl (triphenylmethyl)

CF3CO-

Mal

PhNHCS- or PtcPht or Pht <

Pht-

Tos-

(see

Note i)

Ph3C or Trt

Notes
i) In organic nomenclature (C404.1 of [14]), 'succinyl' signifies the bivalent group formed from succinic acid by removal of both hydroxyl
groups, but in biochemical usage it usually signifies the 3-carboxypropanoyl group, e.g. succinyl-CoA.
ii) The use of D for 'di' and T for 'tn' and 'tetra' is discouraged if these apply to atoms or groups for which simple symbols exist, e.g. in
CF3CO, Me3Si and H4folate. We feel less strongly when their avoidance involves giving unusual meanings to symbols, e.g. N for nitro, so Dnp

and N2ph are offered as alternative symbols for dinitrophenyl. See also Note ii of 3AA-15.2.5.
iii) The symbol HCO is preferred to CHO for the formyl group, because CHO has sometimes been used to indicate the attachment of
carbohydrate.

3AA-18.2. Principles of Symbolizing Substituent Groups and Reagents

Many reagents used in peptide and protein chemistry for modifying (often protecting) amino, carboxyl and side-chain groups
in amino-acid residues have been designated by a variety of acronymic abbreviations, too numerous to list here. Extensive and

PAAC

6/D

614

IUPAC-IUB JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE

A Table 4. Substituents at the carboxyl group

Group
Benzotriazol-1-yloxy
Benzyloxy

Symbol

Name of glycine derivative (see note)

OBt

1-(Glycyloxy)benzotriazole
Glycine benzyl ester

OCH2Ph

(orOBzl, see note in 3AA-18.1)

OCMe3 or
OCHPh2 or OBzh

tert-Butoxy
Diphenylmethoxy

Ethoxy
Methoxy
4-Nitrobenzyloxy
4-Nitrophenoxy
4-Nitrophenylthio
Pentachiorophenoxy
Phenylthio
Quinolin-8-yloxy
Succinimido-oxy
2,4,5-Trichiorophenyloxy

OEt
OMe
ONb
ONp
SNp
OPcp
SPh
OQu

ONSu or OSu
OTcp

Glycine t-butyl ester

Glycine diphenylmethyl ester
(or benzhydryl ester)
Glycine ethyl ester
Glycine methyl ester
Glycine 4-nitrobenzyl ester
Glycine 4-nitrophenyl ester
Thioglycine S-(4-nitrophenyl ester)
Glycine pentachlorophenyl ester
Thioglycine S-(phenyl ester)
Glycine quinolin-8-yl ester
N-(Glycyloxy)succinimide
Glycine 2,4,5-trichiorophenyl ester

Note. Carboxyl substituents will not normally appear as prefixes in the names of derivatives of amino acids or peptides, so the name of the
group, its prefix name, given in column 1, is little used in naming compounds. Column 3 is therefore given to show how derivatives containing the
group are named (by one of the alternative methods of 3AA-9.1).

indiscriminate use of such abbreviations is discouraged, especially when the accepted trivial name of the reagent is short, e.g. tosyl

chloride, trityl chloride, etc.

It can be useful to symbolize a reagent in such a way that the group transferred retains its identity in a reaction, e.g.
-+ Dns-Gly
+H + +Cl Dns-Cl + Gly
Dnp-F +NH2-R

- Dnp-NH-R+H +F

For this reason DnsCl is usually preferred to DNS for dansyl chloride (although the full name is short enough for most textual

use), and DnpF to the original FDNB for i-fluoro-2,4-dinitrobenzene, and similarly Nbs2 in place of DTNB for 3,3'dithiobis(6-nitrobenzoic acid) (Ellman's reagent) and (PrO)2P0F or DipF for diisopropyl fluorophosphate.
Symbols constructed from known elements are more readily understood than arbitrary abbreviations, e.g. Tos-Arg-OMe
rather than TAME for tosylarginine methyl ester, and Tos-Phe-CH2C1 rather than TPCK for 'tosylphenylalanine chloromethyl

ketone', a name incorrectly used for tosylphenylalanylchloromethane (3AA-1O.2), but misleading because it erroneously
specifies the carbonyl group twice.

3AA-19. PEPTIDE SYMBOLISM

3AA-19.i. Peptide Chains

The amino-acid symbols were developed for representing peptide sequences (3AA-16). Peptides containing bonds other than
between C-i and N-2 of adjacent residues are also easily represented (3AA-16 to -18). Examples:
Glycylglycine
N-a-Glutamylglycine

Gly-Gly
Glu-Gly

N-y-Glutamylglycine

Glu

Thyroliberin
Angiotensin II

Glp-His-Pro-NH2
Asp-Arg-Val-Tyr-Ile-His-Pro-Phe

Glutathione

Glu

-Gly
or Giu

or Glu 1-Gly or Glu(-Gly)

LGly

or G u Cys-Gly or Glu(-Cys-Gly)

LcysGly
Note. Glu

would represent the corresponding thiol ester with a bond between the y-carboxyl of glutamic acid and the

Cys-Gly
thiol group of cysteine.

Nomenclature and symbolism for amino acids and peptides

N2-a-Glutamyllysine

Glu-Lys

N6-a-Glutamyllysine

G1u or Glu Lys

615

Lys

N2-y-Glutamyllysine

or Glu Lys

Glu

LLys
N6-y-Glutamyllysine

II

Glu or Glu Lys or Glu Lys

Lys

for modified residues or names of compounds may be used in such formulas. Thus a peptide with a C-terminal
aldehyde may be shown using either a name or a symbol constructed according to 3AA-16.3. Example:
Symbols

Ac-Leu-Leu-argininal or Ac-Leu-Leu-Arg-H

(If the second method is used, the symbol should be explained to avoid confusion.)
A
If part of a sequence is unknown, but its composition can be specified, this may be indicated by parentheses, with commas
between the residues listed as present, e.g. Ala-Lys-(Ala,Gly3,Val2)-Glu-Val.
A
Ifa peptide must be written on more than one line, we advise placing a hyphen at the end ofeach line to be continued (where it
has its usual meaning of a continuation symbol), and also at the start of the next line (where it represents the peptide bond), e.g.
Ala-Ser-Tyr-Phe-Ser-Gly-Pro-Gly-Trp-Arg

In diagrams the two lines can usually be joined, as in

Ala-Ser-Tyr-Phe-LGlyproGlyTrpArg'
but such a break may also be needed in textual material where this is not possible.

3AA-19.2. Use of Configurational Prefixes

Residue symbols written in a sequence denote the L configuration for chiral amino acids, unless otherwise indicated (3AA14.5). A D residue is shown by inserting a D before the symbol, separated from it by a hyphen (which may be omitted to make the
number of residues appear more clearly).
The symbol DL signifies a racemic mixture, so should not occur in the designation of peptides with more than one chiral
residue; coupling of a DL-amino acid with a chiral peptide leads to a mixture of diastereoisomeric products whose ratio may
A depend on the conditions of the reaction and will not in general be unity. To indicate that both are present, ambo may be used
(3AA-13.2), and thus the mixture of products formed by acylating L-leucine with DL-alanine may be represented as ambo-AlaLeu, and a mixture of Phe-Ala-Leu and Phe-D-Ala-Leu may be represented as Phe-ambo-Ala-Leu.

A A residue of unknown configuration may be indicated by the prefix c

(Greek

xi), e.g. -Ala.

3AA-19.3. Representation of Charges on Peptides

It is usually convenient to use the same abbreviated formula for a peptide regardless of its state of ionization. To indicate or
stress the charges on a peptide, plus and minus signs may be placed over residues with charged side chains and on either side of the
formula to represent charged termini, e.g.
+

Gly-Glu-Ala-Lys-Cys-Val

and its form in alkali: Gly-Glu-Ala-Lys-Cys-Val -

Such signs may be circled for clarity.

If, however, it is desired to indicate charge by formal modification of the symbols for residues, this may be done as follows.
i) Protonation of the N-terminus. The sign + H is placed beside the symbol for the N-terminal residue without a hyphen between (since a
hyphen would signify removal of H). This gives, for example, HGly-. We prefer this to the alternative recommendation [10] of adding H2-, to
give, for example, + H2-Gly-, because it seems artificial to remove one hydrogen before adding two, and because the hyphen here fails to represent
a single bond.
ii) Deprotonation of the C-terminus. The symbol -o - is placed on the right of the C-terminal residue. Its hyphen signifies removal of -OH

from the carboxyl group, so this is replaced by -0.

iii) Protonation of Side-Chain basic groups. 'H 'is placed above the amino-acid symbol in the two-line representation, or after it, eg. LysH ,

in the one-line system. No lines or parentheses are used, since they would imply removal of H. In earlier [10] recommendations 'H' was added
with a vertical line or parentheses, but again (cf. i) the line represented no single bond.

616

IUPACIUB JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE

iv) Deprotonation of Side-Chain Acidic Groups. The symbols Asp and Glu may have 0 placed at the end of a vertical line above or below
them, or in parentheses after them (cf. ii), since 0 replaces the OH removed. Other acidic residues, e.g. Cys, have the charge alone at the end of
the vertical line or in parentheses, since the group removed here is H.

Hence the two ionic forms shown above for a peptide could be drawn as

H
+ HG1y-Glu-Ala-Lys-Cys-Val-0
An isoelectric form of Gly-Lys-Gly could be drawn as

I
and Gly-Glu-Ala-Lys-Cys-Val-0
I

H+

Gly-Lys-Gly-0

whereas its dihydrochloride could be drawn as

HGly-Lys-Gly-OH 2 Cl

3AA-19.4. Peptides Substituted at N-2 (see 3AA-16.2 and -17.1)

NO

NO
or Gly__LGly
Me

Glycylnitrosoglycine

Gly Gly

Glycylsarcosine (see Appendix)

Gly-Sar or G1yGly or Gly__LGly

Ac
Ac

Glycyl-N-acetylglycine

(dy Gly

or Gly

Me

ly

Gly\

Gly-1
Gly--Gly or Gly1Gly

N,N-diglycylglycine

3AA-19.5. Cyclic Peptides

3AA-19.5.1. Homodetic Cyclic Peptides

Cyclic peptides in which the ring consists solely of amino-acid residues in eupeptide linkage may be called homodetic cyclic
peptides. Three representations are possible:
i) The sequence is formulated in the usual manner but placed in parentheses and preceded by 'cyclo'. Example: gramicidin S
cyclo(-Val-Orn-Leu-D-Phe-Pro-Val-Orn-Leu-D-Phe-Pro-)

or (see 3AA-19.2, sentence 2)

cyclo(-Val-Orn-Leu-DPhe-Pro-Val-Orn-Leu-DPhe-Pro-)

ii) The sequence is again written in one line, but the residues at each end of the line are joined by a lengthened bond, e.g.

LValOrnLeuDpheproyalOrnLeuDpheprol
or (3AA-19.2, sentence 2)

r0rneuProa0rneu0Ph0i
iii) The residues are written on two lines, so that the sequence is reversed on one of them. Hence the CO to NH direction
within the peptide bond must be indicated by arrows (3AA-16.2 and -16.3). Hence gramicidin S may by written (using the option of

3AA-19.2, sentence 2):

Val*OrnLeu* DPhePro
Pro4DPhe4--Leu4OrnVal

3AA-19.5.2. Heterodetic Cyclic Peptides

Heterodetic cyclic peptides are peptides consisting only of amino-acid residues, but the linkages forming the ring are not
solely eupeptide bonds; one or more is an isopeptide, disulfide, ester, or other bond.
Their symbolic representation follows logically from that of substituted amino acids (3AA-16.4). Examples:
Oxytocin

Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly-NH2

Cyclic ester of threonylglycylglycylglycine Thr-Gly-Gly-Gly or (3AA-1 7.6) H-Thr-Gly-Gly-Gly

Nomenclature and symbolism for amino acids and peptides

3AA-19.6.

617

Depsipeptides

Depsipeptides are oligomers formed from amino acids and other bifunctional acids, usually hydroxy acids. They are often
cyclic. In symbolic representation, any special symbols used for the hydroxy acids should be defined.
3AA-19.7. Peptide Analogues

Analogues ofpeptides in which theCONHgroup thatjoins residues is replaced by another groupingmay be indicated [25]
by placing a Greek psi, followed by the replacing group in parenthesis, between the residue symbols where the change occurs.
Examples:
Ala-(NH - CO) Ala
for NH -CHMe -NH -CO CHMe C00
for NH CHMe CH = CHCHMe C00
Ala-t'(CH = CH, trans)-Ala

3AA-19.8. Alignment of Peptide and Nucleic-Acid Sequences

A Although hyphens between residues are important in representing peptide sequences (3AA-16), they may be omitted (I) ifit is
necessary to align sequences with those of nucleic acids ; this is an alternative to separating triplets (II):

MetSerlleGinHis
(I)

Part

AGTATGAGTATTCAACAT
TCATACTCATAAGTTGTA

Met-SerIleGin-His
(II)

AGT ATG AGT ATT CAA CAT

TCA TAC TCA TAA GTT GTA

2, Section B: THE ONE-LETTER SYSTEM (revision and updating of [11])

3AA-20. THE NEED FOR A CONCISE REPRESENTATION OF SEQUENCE

3AA-20.1 . General Considerations Regarding the One-Letter System

There are difficulties in using the three-letter system (3AA-14 to 3AA-19) in presenting long protein sequences. A one-letter

code is much more concise, and is helpful in summarizing large amounts of data, in aligning and comparing homologous
sequences, and in computer techniques for these processes. It may also be used to label residues in three-dimensional pictures of
protein molecules.
The possibility of using one-letter symbols was mentioned by Gamow & Yeas [26] in 1958. orm et al. [27] systematized the
idea in 1961 (see, for example, [28]), and Dayhoff and Eck used one-letter symbols derived partly from the code of orm et al. in
their compilations of protein sequences ([29], latest edition [30]). IUB-IUPAC recommendations [11] were approved in 1968 on
the basis of proposals of a subcommittee of W. E. Cohn, M. 0. Dayhoff, R. V. Eck, and B. Keil, and these recommendations are
given here with no substantial change.
3AA-20.2. Limits of Application of the One-Letter System
The one-letter system is less easily understood than the three-letter system by those not familiar with it, soit should not be used
in simple text or in reporting experimental details of sequence determination. It is therefore recommended for comparisons of
long sequences in tables and lists, and in other special uses where brevity is important. If both it and the single-letter system for
nucleotide sequences [23] are used in the same paper, particular care should be taken to avoid confusion.
3AA-21. DESCRIPTION OF THE ONE-LETTER SYSTEM

3AA-21.1. Use of the Code

The letter written at the left-hand end is that of the amino-acid residue carrying the free amino group, and the letter written at
the right-hand end is that of the residue carrying the free carboxyl group. The absence of punctuation beyond either end of a
sequence implies that the residue indicated at that end is known to be terminal. A fragmentary sequence is preceded or followed
by a slash (I) if its end is not known to be the end of the complete molecule.

3AA-21.2. The Code Symbols

The symbols are listed, in alphabetical order of amino-acid names, in Table 1. Table 5 gives them in alphabetical order of
symbols.
Note on the Choice of Symbols

Initial letters of the names of the amino acids were chosen where there was no ambiguity. There are six such cases: cysteine, histidine,
isoleucine, methionine, serine and valine. All the other amino acids share the initial letters A, G, L, P or T, so arbitrary assignments were made.
These letters were assigned to the most frequently occurring and structurally most simple of the amino acids with these initials, alanine (A),
glycine (G), leucine (L), proline (P) and threonine (T).
Other assignments were made on the basis of associations that might be helpful in remembering the code, e.g. the phonetic associations ofF
forphenylalanine and R for arginine. For tryptophan the double ring of the molecule is associated with the bulky letter W. The letters N and Q

618

IUPACIUB JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE

Table 5. The 0ne-Letter Symbols

One-letter
symbol

Three-letter
symbol

Amino acid

Ala
Asx

alanine
aspartic acid or asparagine
cysteine
aspartic acid
glutamic acid
phenylalanine
glycine
histidine
isoleucine

B
C

Cys

Asp

Glu
Phe
Gly
His

Ile

Lys

lysine
leucine
methionine
asparagine

Pro
GIn
Arg

proline
glutamine
arginine
serine
threonine

L
M

Q
R
S

Leu
Met
Asn

Ser

Thr

Val
Trp

X
Y
A Z

Xaa
Tyr
Glx

valine

tryptophan
unknown or 'other' amino acid
tyrosine
glutamic acid or glutamine (or substances

such as 4-carboxyglutamic acid and 5oxoproline that yield glutamic acid on acid
hydrolysis of peptides)

were assigned to asparagine and glutamine respectively; D and E to aspartic and glutamic acids respectively. K and Y were chosen for the two
remaining amino acids, lysine and tyrosine, because, of the few remaining letters, they were close alphabetically to the initial letters of the names.
U and 0 were avoided because U is easily confused with V in handwritten material, and 0 with G, Q, Cand D in imperfect computer print-outs,
and also with zero. J was avoided because it is absent from several languages.
Two other symbols are often necessary in partly determined sequences, so B was assigned to aspartic acid or asparagine when these have not
been distinguished; Z was similarly assigned to glutamic acid or glutamine. X means that the identity of an amino acid is undetermined, or that the
amino acid is atypical.

3AA-21.3. Spacing
An important use of the one-letter notation is in presenting alignment of homologous sequences. It is therefore vital not to
destroy alignment by variable punctuation or variable width of letters. A single space is therefore left between symbols, as a blank

if not occupied by punctuation (3AA-21 .4 and 21.5), so that such punctuation can be inserted without destroying alignment.
Exactly the same spacing is given to each letter, each blank and each punctuation mark, as in typewritten material or, if printed, as
in 'typewriter type font'.
3AA-21 .4. Known Sequences

A blank between letters indicates that the sequence was determined experimentally. For example,
A C D E F G H I K L M N P Q means Ala-Cys-Asp-Glu-Phe-Gly-His-Ile-Lys-Leu-Met-Asn-Pro-Gln

3AA-21 .5. Punctuation in Partly Known Sequences

Parentheses are used to indicate regions of a sequence in which the composition is known, but the sequence undetermined;
they are also placed round the symbol for a single residue to show that its identification is tentative. The one-space symbol '= 'can

be used for')(' to indicate the end of one unknown sequence and the beginning of another.
If the residue inside parentheses can be positioned with confidence by homology with related proteins, the letters are
separated by dots. If their position is arbitrary for lack of even indirect evidence the letters are separated by commas. A slash (/)
may be used to separate the symbols for residues that have not been shown experimentally to be corrected, because they are derived
from different peptides. A slash before or after a sequence shows that termination has not been demonstrated (3AA-21 .1).

Nomenclature and symbolism for amino acids and peptides

This punctuation

619

is illustrated in the comparison ofthree sequences, where two partly known (ac) are aligned with a known

one (b):

a)

(A,C,D)E F G(H.I.K.L=M,N)P Q

b)

RSTEFGHIKLADPQ

C)

A C D E F/G H I K L(M,N)P Q

Thusthe sequence ofone ofthe fragments (H.I.K.L) can be inferred with confidence for(s) whereas that offragments (A,C,D) and

(M,N) cannot. Two fragments were sequenced independently in (c). Their positioning is made only by analog with (b).
If more elaborate punctuation is required for special circumstances, it is essential that only one character (or a blank of similar
size) should appear between the letters of the code.
Part 3. Modification of Named Peptides (a revision and updating of [12])
3AA-22. NAMES AND SYMBOLS FOR DERIVATIVES OF NAMED PEPTIDES

It is often convenient to specify the structure of a peptide by reference to a named sequence of which it is a variant. The
recommendations that follow allow this, but they apply only to modifications of the sequence involving normal amide links
between residues.
Note. To exemplify any named peptide, the imaginary peptide 'iupaciubin' (to symbolize the harmonious co-operation of
IUPAC and IUB), Ala-Lys-Glu-Tyr-Leu, is used in formulating the recommendations below.
3AA-22.1. Replacement of Residues

In a peptide of trivial name iupaciubin, if the qth amino-acid residue, starting from the N-terminal end of the chain, is replaced by the amino acid Xaa, the semitrivial name of the modified peptide is [q-amino acid]iupaciubin, and the abbreviated form
is [Xaa"]iupaciubin. A designation of the chain may be placed before the residue number, e.g. [A1aB12]insulin(cattle) (see
Comment f). Examples:
[8-Citrulline]vasopressin,

[Cit8]vasopressin;

[5-Isoleucine,7-alanine]angiotensin II,

[Ile5,A1a7]angiotensin II.

Notes
a) In the full name, the replacement amino acid is designated by its residue name, not the name of its acyl group (e.g. glycine,
not glycyl). This name, and the position of replacement, are given in square brackets.
b) In the abbreviated form, the amino-acid residues are designated by standard 3-letter symbols (Table 1), the first letter only
being a capital (3AA-14), in square brackets.
c) In the abbreviated form the position of substitution is indicated in a special fashion, i.e. by a superior numeral, to indicate
that it is a residue, not an individual atom, that is being replaced.
d) The residue replaced is not designated in these semitrivial names in order to keep the names short, and because this form of
nomenclature of 3AA-22. 1 clearly differs from ordinary substitution nomenclature.
e) The replacement of an amino-acid residue by its enantiomer may be shown by application of this rule as follows: the
A replacement in iupaciubin of L-tyrOsine at position 4 by D-tyrosifle results in [4-D-tyrosine]iupaciubin with the abbreviations

[D-Tyr4]iupaciubin. A mixture of this with iupaciubin gives [4-ambo-tyrosine]iupaciubin or [ambo-Tyr4]iupaciubin (3AA-13.2 and
3AA-19.2). Examples: [o-Ser1]corticotropin; [o-Asp1]angiotensin II.
f) Specification of a sequence may require the species as well as the peptide to be named. If so, the name of the species should be
attached, in parenthesis, to the name of the peptide whenever a modifying prefix is present. Thus a substitution in cattle insulin
could give [A1aB1 2]insulin(cattle). (We prefer 'cattle' as the adjective for this species, since 'bovine' is not used in common speech to

designate the species, but to compare human attributes with those of the cow, and 'ox' can be misleading.)
g) It may be convenient to represent replacement of Gln by Glu or of Asn by Asp with the prefix 'desamido'. Thus
[Glu30]corticotropin(pig) could be called desamido30-corticotropin(pig). Similarly replacement of Gla by Glu can be designated
with the prefix 'decarboxy'.
3AA-22.2. Extension of the Peptide Chain
The compounds obtained by extension of a peptide at either the N-terminus on the C-terminus are designated by the kinds of
names and abbreviations shown below; these are in accordance with general principles of peptide nomenclature (3AA-13.1).
Examples:
a) Extension at the N-terminus
Aminoacyliupaciubin
Valyliupaciubin
Valylglycyliupaciubin
(for extension by two residues)

Xaa-iupaciubin
Val-iupaciubin
Val-Gly-iupaciubin

620

IUPAC-IUB JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE

b) Extension at the C-terminus

lupaciubinylamino acid

Iupaciubmyl-Xaa

lupaciubinylleucine

Iupaciubinyl-Leu

A This rule is not directly applicable to extension at the C-terminus ofnatural peptides that possess a terminal amide group, such
as oxytocin and a-melanotropin. For these, a new name should be given to the corresponding peptide with a free carboxyl group
by adding 'oic acid' to the trivial name, e. g. oxytocinoic acid from oxytocin, so that extension can then be denoted as above, e.g.
oxytocinoyl-Xaa.

Note
The enkephalins are the two peptides Tyr-Gly-Gly-Phe-Leu and Tyr-Gly-Gly-Phe-Met. Designations such as Leu-, leucyl-

and leucine-enkephalin have been given to the former, with corresponding teim for the latter. These all wrongly imply
N-terminal extension, and could not be used together with any indication of such extension. Morley [25] has advocated
[Leu]enkephalin, if necessary [Leu5}enkephalin, in accordance with 3AA-22.1, implying that enkephalin means Tyr-Gly-GlyPhe-Xaa. We believe that [Leu5]enkephalin is the best designation.
3AA-22.3. Insertion of Residues

The compound obtained by insertion of an additional amino-acid residue Xaa in the position between the qth and the (q + 1)th

residue of the peptide iupaciubin is named endo-qa-amino acid-iupaciubin (abbreviated form:

Example:
endo-4a-tyrosine-angiotensin II,

endo-Tyr4-angiotensin II.

Notes
a) This form has analogies in other fields where endo iniplies the insertion of something into a structure (e.g. endo-methylene).
The prefix or index qa is based on analogies with the steroids where the atoms inserted into a ring after atom no. q are designated

qa, qb, etc.

b) The prefix 'homo' is not suitable for designating the insertion of a whole residue, especially since it is commonly used to
modify the names of individual amino acids, e.g. homoserine (3AA-2.3).
c) Multiple insertions, and insertion of two or more residues together in the same place in the chain, are shown by a logical
extension of this recommendation. Thus the insertion into the peptide iupaciubin of threonine between residues I and 2, and of
valine and glycine (in that order) between residues 4 and 5, is shown by the name 'endo-la-threonine,4a-valine,4b-glycineiupaciubin' and the abbreviation endoThrla,Valsa,Gly4liupaciubin.
3AA-22.4. Removal of Residues

The compound obtained by the formal removal of an amino-acid residue from the peptide iupaciubin in position q is
designated by the name des-q-amino acid-iupaciubin, abbreviated des-Xaa5-iupaciubin. Example:
des-7-proline-oxytocin,

des-Pro7-oxytocin

Notes

a) Removal of a whole residue is indicated in a way similar to that for removal of a ring in steroids, e.g. des-A-androstane.
b) The form 'de' is not suitable as a prefix because it is easily confused, in speaking, with D (for configuration).
c) Multiple deletions are designated similarly, e.g. des-Ile3,Asn5-oxytocin. If a complete sequence is to be removed, the first
and last loci of this sequence are all that need be specified, and they should be put in parentheses with a hyphen between them, e.g.
des-(B24-B28)-insulin(mouse).
3AA-22.5. Substitution of Side Chains of Residues

The compound formed by introducing an additional amino-acid residue as a substituent of the side chain of a residue in a
peptide is named by applying the rules of peptide nomenclature (3AA-7, -9 and -13) to the trivial name, as follows.

22.5.1. Acylation of a Side-Chain Amino Group

If the additional residue acylates an amino group of a peptide, the name of the additional amino acid is written, in its acyl
group form (3AA-9.3), and prefixed by symbols indicating the position of substitution (atom and residue number, see 3AA-13.4).

Example: the imaginary compound

Va!1

Ala-Lys-Glu-Tyr-Leu

Nomenclature and symbolism for amino acids and peptides

621

by acylation of the i-amino group of the lysine residue at position 2 of iupaciubin (Ala-Lys-Glu-Tyr-Leu) with a valyl
group is named NE2va1y1iupaciubin (abbreviated N2-Va1-iupaciubin).
derived

22.5.2. Other Substituents Named as Prefixes

Other substituents that can be named as prefixes are treated similarly to amino acyl groups. Examples:
Me
N62-Methyliupaciubin

for

Ala-Lys-Glu-Tyr-Leu
COOH

C43-Carboxyiupaciubin for Ala-Lys-Glu-Tyr-Leu

(alternative to replacement with Gla under 3AA-22.1)
SO3H

044-Sulfoiupaciubin or iupaciubin 044-sulfate for Ala-Lys-Glu-Tyr-Leu

04'2-Sulfogastrin or gastrin 04'2-sulfate for gastrin II.

N' NB29bis(Boc)insulin

or

N2hl,NSB29bis(Boc)insulin

22.5.3. Acylation by a Side-Chain Carboxyl Group

If an additional amino acid is joined by amide formation between its 2-amino group and the side-chain carboxyl of the peptide
iupaciubin, so that the additional amino acid has a free 1-carboxyl group, the derivative is named by specifying the position of
substitution (atom and residue number, 3AA-13.4) and it is given the designation 'iupaciubinyl-amino acid'.
Example: the imaginary compound
AIa-Lys-Glu-Tyr-Leu
in which

valine is acylated by the y-carboxyl group of a glutamic residue in position 3 (Glu-3) of iupaciubin (Ala-Lys-Glu-TyrLeu), is named N(iupaciubinC3yl)valine, or N-(iupaciubin-C53-yl)valine, abbreviated to iupaciubin-C53-yl-Val.
Prefixes may also need to be formed from peptide names for use as substituents in other types of compound, as described in
3AA-13.5.

3AA-22.6. Partial Sequences (fragments)

A A peptide derived from a named peptide iupaciubin by removal of all residues before thepth and all after the qth is named as
iupaciubin-(p-q)-peptide. Examples:
From a-melanotropin
Ac-Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp- Gly-Lys-Pro-Val-NH2

12345678910111213

we may have
Met-Glu-His-Phe-Arg-Trp-Gly
10
4

or

a-melanotropin-(4-10)-peptide

or, to illustrate the naming of a peptide that contains two fragments, and also a C-terminal amide group:
His-Phe-Arg-Lys-Pro-Val-NH2 may be called

cx-melanotropin-(6-8)-(11-13)-peptide amide.

For oligopeptides it may be convenient to state the length of peptide, e.g. iupaciubin-(2-4)-tripeptide, but this is not normally
useful for peptides of over about twelve residues, because the larger multiplying affixes are not widely known. Such a check on the
number of residues is particularly useful when two or more sequences are joined, e.g. a-melanotropin-(6-8)-(11-13)-hexapeptide

amide.
3AA-22.7. Peptides with Reversed Sequence and Enantiomers

The peptide whose sequence is the reverse of a named peptide may itself be named with the prefix 'retro-', giving retroiupaciubin from iupaciubin. The enantiomer of a named peptide may be specified with the prefix 'ent-' (a contracted form of
enantio-, F-6.4 of [15]), giving ent-iupaciubin from iupaciubin.

3AA-22.8. Peptide Analogues

Analogues of peptides in which the CONH group that connects two residues is replaced by another group (3AA-19.7) may
be indicated by placing i/i in square brackets before the name [25]. The f is placed between superscripts indicating the residues
modified, and is followed by a comma and the replacing group, e.g. [3iJ4,CH2-S]iupaciubin.

622

IUPACIUB JOINT CONNISSION ON BIOCUEMICAL NOMENCLATURE

Summary of Modification Nomenclature

The application of the principles of 3AA-22 is illustrated in Table 6.

3AA-22.9.

Table 6. App/ication of the methods of modifying named peptides

Operation

Short name

Structure

lupaciubin

Ala-Lys-Glu-Tyr-Leu

22.1

Replacement

[Phe4]iupaciubin

Ala-Lys-Glu-Phe-Leu

22.2a

Extension (N-terminal)

Arg-iupaciubin

Arg-Ala-Lys-Glu-Tyr-Leu

22.2b

Extension (C-terminal)

lupaciubinyl-Met

Ala-Lys-Glu-Tyr-Leu-Met

22.3

Insertion

Endo-Thr2-iupaciubin

Ala-Lys-Thr-Glu-Tyr-Leu

22.4

Removal

Des-G1u3-iupaciubin

Ala-Lys-Tyr-Leu

Section

223
2

Val
22.5.1

Side-chain substitution on amino group

N2-Val-iupaciubin

Ala-Lys-Glu-Tyr-Leu

22.5.2

Side-chain substitution on carboxyl group

C43-Iupaciubinyl-Val

Ala-Lys-Glu-Tyr-Leu

22.6
22.7

Partial sequence
Reversal of sequence

Iupaciubin-(2-4)-peptide
retro-lupaciubin

Lys-Glu-Tyr
Leu-Tyr-Glu-Lys-Ala

22.7

Enantiomer

ent-lupaciubin

D-Ala-D-Lys-D-Glu-D-Tyr-D-Leu

22.8

Replacement of CONH of peptide bond

[3i4,CH2S]iupaciubin

Ala-Lys-Glu-fi(CH2S)-Tyr-Leu

Val

* Square brackets are required to indicate replacement, but are not used for most other modifications.

REFERENCES
1. Vickery, H. B. & Schmidt, C. L. A. (1931) Chem. Rev. 9, 169318.
2. Vickery, H. B. (1972) Adv. Protein Chem. 26, 81 171.
3. Vickery, H. B. (1947) J. Biol. Chem. 169, 237 245.
4. International Union ofPure and Applied Chemistry(IUPAC), Definitive Rules for the Nomenclature ofAmino Acids (1960)J. Amer. Chem.
Soc. 82, 55755577.
5. Vickery, H. B. (1963) J. Org. Chem. 28, 291 293.
6. IUPAC Commission on the Nomenclature of Organic Chemistry (CNOC) and IUPAC-IUB Commission on Biochemical Nomenclature
(CBN), Nomenclature ofoc-Amino Acids, Recommendations 1974, Biochem. J. 149, 1 16(1975); Biochemistry, 14, 449 462(1975); Eur.
J. Biochem. 53, 1 14 (1975); also pp. 6477 in [7].

7. International Union of Biochemistry (1978) Biochemical Nomenclature and Related Documents, The Biochemical Society, London.
8. Brand, E. & Edsall, J. T. (1947) Annu. Rev. Biochem. 16, 223 272.
9. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), Abbreviated Designation of Amino-Acid Derivatives and Peptides,
Recommendations 1966, Arch. Biochem. Biophys. 121, 1 5 (1967); Biochem. J. 102, 23 27(1967); Biochemistry, 5, 2485 2489 (1966);
Biochim. Biophys. Acta, 121, 1 7 (1967); Bull. Soc. Chim. Biol. 49, 121 129 (1968) (in French); Eur. J. Biochem. 1, 375 378 (1967);
Hoppe-Seyler's Z. Physiol. Chem. 348,256261 (1967)(in German); J. Biol. Chem. 241, 2491 2495 (1966); Mol. Biol. 2,282288(1968)

(in Russian).
10. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), Symbols for Amino-Acid Derivatives and Peptides, Recommendations
1971, Arch. Biochem. Biophys. 150, 1 8 (1972); Biochem. J. 126, 773 780 (1972), corrected 135,9(1973); Biochemistry, 11, 17261732
(1972); Biochim. Biophys. Acta, 263, 205 212(1972); Eur. J. Biochem. 27, 201 207(1972), corrected 45, 2(1974); J. Biol. Chem. 247, 977
983 (1972); Pure Appl. Chem. 40, 315 331 (1974); also pp. 7884 in [7].
11. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), A One-Letter Notation for Amino Acid Sequences, 1968, Arch. Biochem.
Biophys. 125(3),i v(1968);Biochem.J. 113,1 4(1969);Biochemistry, 7,2703 2705(1968);Biochim. Biophys. Acta, 168,610(1968);
Bull. Soc. Chim. Biol. 50, 15771582 (1968) (in French); Eur. J. Biochem. 5, 151 153 (1968); Hoppe-Seyler's Z. Physiol. Chem. 350, 793
797 (1969) (in German); J. Biol. Chem. 243, 35573559 (1968); Mol. Biol. 3,473477 (1969) (in Russian); Pure Appl. Chem. 31, 641
645 (1972), also pp. 91 93 in [7].

12. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), Rules for Naming Synthetic Modifications of Natural Peptides, 1966,
Arch. Biochem. Biophys. 121, 68 (1967); Biochem. J. 104, 1719 (1967), corrected 135, 9 (1973); Biochemistry, 6, 362 364 (1967);
Biochim. Biophys. Acta, 133, 1 5 (1967); Bull. Soc. Chim. Biol. 49, 325 330 (1967) (in French); Eur. J. Biochem. 1, 379 381 (1967),
corrected 45, 3 (1974); Hoppe-Seyler's Z. Physiol. Chem. 348, 262 265 (1967) (in German); J. Biol. Chem. 242, 555557 (1967);Mol.
Biol. 2, 466 469 (1968) (in Russian); Pure Appl. Chem. 31, 647 653 (1972); also pp. 8587 in [7].
13. IUPAC Commission on Nomenclature of Organic Chemistry (CNOC), Nomenclature of Organic Chemistry, Section E: Stereochemistry,
Recommendations 1974, Pure Appl. Chem. 45, 1130 (1976); also pp. 118 in [7] and pp. 473 490 in [14].

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624

IUPAC-IUB JOINT CONNISSION ON BIOCHEMICAL NOMENCLATURE

Appendix. Amino Acids with Trivial Names (excluding those listed in Table 1)
It is often helpful to use trivial names in order to avoid cumbersome systematic or semisystematic names, particularly if the substance has to be

named frequently. Coining of trivial names is treated in 3AA-2.1, and a number of existing trivial names are listed in the appendices to the
previous edition of recommendations on amino-acid nomenclature [6]; only the commoner are listed here.
Trivial name

Symbol

Structure of substance or of derived ion in the form

predominating at neutral pH
f3Ala

NH3CH2 CH2 COO

Allysine

HCO[CH2]3CH(NH3)COO

Citrulline

Cit

NH2 CONH[CH2]3CH(NH3)COO

Cystathionine

Ala

/3-Alanine

Hcy
Cysteic acid

Cya

Cystine

Cys
Cys

Dopa

CH2CH(NH3)COO
S[CH2]2CH(NH3)COO

03SCH2CH(NH3ICOO
SCH2CH(NH3)COO

SCH2-CH(NH3)COO

HO

HOCH2-CH(NH3)COO
Homocysteine

Hcy

HSCH2 CH2 CH(NH3)COO

Homoserine

Hse

HOCH2CH2 CH(NH3COO

Homoserine lactone

Hsl

t5CH2CH2CH(NH3ICO

Lanthionine

Ala
H2CH(NH3)COOCys

SCH2CH(NH3)COO

Ornithine

Orn

NH3[CH2]3CH(NH3iCOO

5-Oxoproline

Glp

NHCOCH2 CH2CHC00

Sarcosine

Sar

CH3NH2CH2COO

Thyronine

Thyroxine

Thx HOO* CH2 CH(NH3)COO

HOi

'Oi/I.L CH2CH(NH3)COO